diff --git a/content/guides/running_applications/bioinformatics_tools/_index.md b/content/guides/running_applications/bioinformatics_tools/_index.md
index 08edff591b2c61d59300887455a70c49c225f9a4..7be0897105cff80bb9f898c11712c2217f1ecd02 100644
--- a/content/guides/running_applications/bioinformatics_tools/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/_index.md
@@ -1,15 +1,13 @@
+++
title = "Bioinformatics Tools"
+description = "How to use various bioinformatics tools on HCC machines"
+weight = "52"
+++
-<span style="color: rgb(0,0,0);">The following is a categorized list of
-bioinformatics tools available on HCC. Each page contains summary of the
-tool, information about the HCC resources that have the specific
-tool, links to user documentation, as well as example SLURM submit
-scripts. More detailed information about submitting SLURM jobs and
-checking job status on HCC can be
-found [here](Submitting-Jobs_332222.html).</span>
+The following is a categorized list of bioinformatics tools available on HCC. Each page contains summary of the tool, information about the HCC resources that have the specific tool, links to user documentation, as well as example SLURM submit scripts.
-<span style="color: rgb(0,0,0);"> </span>
+More detailed information about submitting SLURM jobs and checking job status on HCC can be found [here](../../submitting_jobs)
+
+{{% children %}}
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/_index.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/_index.md
index bea2107d1d6e0babe1e34d5224a5437214ea1fb1..385da5f1a1f9889a9364ebe46dbce68e14cccbaf 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/_index.md
@@ -1,18 +1,7 @@
+++
title = "Alignment Tools"
+description = "How to use various alignment tools on HCC machines"
+weight = "52"
+++
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-
-<span id="title-text"> HCC-DOCS : Alignment Tools </span>
-=========================================================
-
-Created by <span class="author"> Adam Caprez</span> on Sep 04, 2014
-
-
-
-
+{{% children %}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
index 490d2449e5f8ed1a994de7b02e276997a4f8c960..1a67b1993108afeeac41dfe413489d6285426c72 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
@@ -1,1175 +1,16 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Alignment Tools](Alignment-Tools_8193288.html)
++++
+title = "BLAST"
+description = "How to use BLAST on HCC machines"
+weight = "52"
++++
-<span id="title-text"> HCC-DOCS : BLAST </span>
-===============================================
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
+[BLAST] (https://blast.ncbi.nlm.nih.gov/Blast.cgi) is a local alignment tool that finds similarity between sequences. This tool compares nucleotide or protein sequences to sequence databases, and calculates significance of matches. Sometimes these input sequences are large and using the command-line BLAST is required.
-| Name | Version | Resource |
-|-------|---------|----------|
-| blast | 2.2.30 | Tusker |
-| blast | 2.4.0 | Tusker |
-
-
-
-| Name | Version | Resource |
-|-------|---------|----------|
-| blast | 2.6.0 | Tusker |
-| blast | 2.7.1 | Tusker |
-
-
-
-| | | |
-|-------|--------|-------|
-| blast | 2.2.29 | Crane |
-| blast | 2.2.30 | Crane |
-| blast | 2.4.0 | Crane |
-
-
-
-| | | |
-|-------|-------|-------|
-| blast | 2.6.0 | Crane |
-| blast | 2.7.1 | Crane |
-
-
-
-BLAST
-(<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi" class="external-link">http://blast.ncbi.nlm.nih.gov/Blast.cgi</a>)
-is a local alignment tool that finds similarity between sequences. This
-tool compares nucleotide or protein sequences to sequence databases, and
-calculates significance of matches. Sometimes these input sequences are
-large and using the command-line BLAST is required.
-
-The following pages, [Create Local BLAST
-Database](Create-Local-BLAST-Database_8193290.html) and [Running BLAST
-Alignment](Running-BLAST-Alignment_8193291.html) describe how to run
-some of the most common BLAST executables as a single job under the
-SLURM scheduler on HCC.
-
-
-
-**Useful Information**
-
-In order to test the BLAST (blast/2.2) performance on Tusker, we aligned
-three nucleotide query datasets, **small.fasta**, **medium.fasta** and
-**large.fasta**, against the non-redundant nucleotide **nt.fasta**
-database from NCBI. Some statistics about the query datasets and the
-time and memory resources required for the alignment are shown on the
-table below:
-
-| | **total \# of sequences** | **total \# of bases** | **total size in MB** | **required time** | **required memory** | \# of used CPUs |
-|------------------|---------------------------|-----------------------|----------------------|-------------------|---------------------|-----------------|
-| **small.fasta** | 41,715 | 35,581,740 | 37.627 MB | \~ 2 hours | \~ 23 GB | 8 |
-| **medium.fasta** | 110,478 | 147,543,113 | 149 MB | \~ 4 hours | \~ 24 GB | 8 |
-| **large.fasta** | 592,593 | 827,629,204 | 836 MB | \~ 15 hours | \~ 47 GB | 8 |
-
-
-
-
-
-
-
-
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_blast\_version.xsl](attachments/8193289/8127538.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/8127539.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_blast\_version.xsl](attachments/8193289/8127540.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/8127541.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17039697.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17039410.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17039458.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17039506.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17039554.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17039604.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17039664.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17039866.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17039754.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193289/17039786.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17039818.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17039996.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17039914.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17039962.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17040044.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040084.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17040132.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040164.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17040214.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040246.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17040358.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040278.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193289/17040310.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040390.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17040438.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040520.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17040486.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17040568.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040631.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17040711.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040663.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040756.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17041090.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040788.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040820.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040902.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040936.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17040969.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17041042.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17041259.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17041156.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17041227.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17041558.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17041510.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17041642.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17041610.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17041785.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17041690.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17041735.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17041824.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17041913.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17041857.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17041950.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17042000.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17042039.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17042090.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17042124.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17042175.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17042244.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17042295.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17042329.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17042380.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17042422.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17042473.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17042511.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17042598.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17042547.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17042634.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17042685.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17042743.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17042794.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17042829.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17042880.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17042970.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17042936.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17043055.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17043004.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17043099.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17043150.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17043235.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17043201.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17043286.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17043325.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17043376.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17043412.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17043463.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17043508.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17043595.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17043544.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17043630.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17043681.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17043751.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17043802.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17043836.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17043887.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17043930.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17043981.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17044020.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17044071.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/17044105.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/17044190.xml) (text/xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193289/35326644.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193289/35326666.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193289/35326824.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193289/16521358.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193289/16521359.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193289/35326901.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193289/35326936.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193289/35327037.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193289/35325378.xml) (text/xml)
+The following pages, [Create Local BLAST Database](create_local_blast_database) and [Running BLAST Alignment](running_blast_alignment) describe how to run some of the most common BLAST executables as a single job using the SLURM scheduler on HCC.
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Useful Information</span>
+In order to test the BLAST (blast/2.2) performance on Tusker, we aligned three nucleotide query datasets, `small.fasta`, `medium.fasta` and `large.fasta`, against the non-redundant nucleotide **nt.fasta** database from NCBI. Some statistics about the query datasets and the time and memory resources used for the alignment are shown on the table below:
+{{< readfile file="/static/html/blast.html" >}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md
index b495506807c68226eda48d4d029773d36c0deecd..a90c0b535b5657d7490533d73a83c94041e07fa7 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/create_local_blast_database.md
@@ -1,484 +1,37 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Alignment Tools](Alignment-Tools_8193288.html)
-7. [BLAST](BLAST_8193289.html)
-
-<span id="title-text"> HCC-DOCS : Create Local BLAST Database </span>
-=====================================================================
-
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
-
-The basic way to create a local BLAST database is to use the
-**makeblastdb** command:
-
-**General Makeblastdb Usage**
-
-``` syntaxhighlighter-pre
-makeblastdb -in input_reads.fasta -dbtype [nucl|prot] -out input_reads_db
-```
-
-where **input\_reads.fasta** is the input file containing all sequences
-that need to be made into a database, and **dbtype** can be either
-*nucl* or *prot* depending on the type of the input file.
-
-Simple example of how **makeblastdb** can be run on Tusker using SLURM
-script and nucleotide database is shown below:
-
-**blast\_db.submit**
-
-\#!/bin/sh
-\#SBATCH --job-name=Blast\_DB
-\#SBATCH --nodes=1
-\#SBATCH --ntasks-per-node=1
-\#SBATCH --time=168:00:00
-\#SBATCH --mem=50gb
-\#SBATCH --output=BlastDB.%J.out
-\#SBATCH --error=BlastDB.%J.err
-
-
-
-| |
-|-----------------------|
-| module load blast/2.7 |
-
-makeblastdb -in input\_reads.fasta -dbtype nucl -out input\_reads\_db
-
++++
+title = "Create Local BLAST Database"
+description = "How to create local BLAST database on HCC resources"
+weight = "10"
++++
+
+
+The basic way to create a local BLAST database is to use the **makeblastdb** command:
+{{< highlight bash >}}
+$ makeblastdb -in input_reads.fasta -dbtype [nucl|prot] -out input_reads_db
+{{< /highlight >}}
+where **input_reads.fasta** is the input file containing all sequences that need to be made into a database, and **dbtype** can be either `nucl` or `prot` depending on the type of the input file.
+
+\\
+Simple example of how **makeblastdb** can be run on Tusker using SLURM script and nucleotide database is shown below:
+{{% panel header="`blast_db.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=Blast_DB
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=BlastDB.%J.out
+#SBATCH --error=BlastDB.%J.err
+
+module load blast/2.7
+
+makeblastdb -in input_reads.fasta -dbtype nucl -out input_reads_db
+{{< /highlight >}}
+{{% /panel %}}
+
+\\
More parameters used with **makeblastdb** can be seen by typing:
-
-**Additional Makeblastdb Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.tusker ~]$ makeblastdb -help
-```
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_blast\_module.xsl](attachments/8193290/8127542.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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-[tusker\_modules.xml](attachments/8193290/35325645.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193290/35326210.xml) (text/xml)
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-[hcc\_modules.xml](attachments/8193290/35326502.xml) (text/xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193290/35326822.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193290/17044365.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193290/35326899.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193290/35326934.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193290/35326953.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193290/35327035.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193290/35325376.xml) (text/xml)
-
-
+{{< highlight bash >}}
+$ makeblastdb -help
+{{< /highlight >}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
index 26b0c81348d95587041ed4322bcca592b984709f..fb2cf5e24cbd1f4a7b2bdaf8e98dfebb6231463b 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
@@ -1,716 +1,121 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Alignment Tools](Alignment-Tools_8193288.html)
-7. [BLAST](BLAST_8193289.html)
++++
+title = " Running BLAST Alignment"
+description = "How to run BLAST alignment on HCC resources"
+weight = "10"
++++
-<span id="title-text"> HCC-DOCS : Running BLAST Alignment </span>
-=================================================================
-
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
Basic BLAST has the following commands:
-- **blastn**: search nucleotide database using a nucleotide query
-- **blastp**: search protein database using a protein query
-- **blastx**: search protein database using a translated nucleotide
- query
-- **tblastn**: search translated nucleotide database using a protein
- query
-- **tblastx**: search translated nucleotide database using a
- translated nucleotide query
+- **blastn**: search nucleotide database using a nucleotide query
+- **blastp**: search protein database using a protein query
+- **blastx**: search protein database using a translated nucleotide query
+- **tblastn**: search translated nucleotide database using a protein query
+- **tblastx**: search translated nucleotide database using a translated nucleotide query
The basic usage of **blastn** is:
-
-**General BLASTN Usage**
-
-``` syntaxhighlighter-pre
-blastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options]
-```
-
-where **input\_reads.fasta** is an input file of sequence data in fasta
-format, **input\_reads\_db** is the generated BLAST database, and
-**blastn\_output.alignments** is the output file where the alignments
-are stored. Additional parameters can be found in the BLAST
-manual: <a href="http://www.ncbi.nlm.nih.gov/books/NBK1763/" class="external-link">http://www.ncbi.nlm.nih.gov/books/NBK1763/</a>,
-or by typing:
-
-**Additional BLASTN Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.tusker ~]$ blastn -help
-```
-
-These BLAST alignment commands are multi-threaded, and therefore using
-the BLAST option **-num\_threads <number\_of\_CPUs>** is
-recommended.
-
-
-
-HCC hosts multiple BLAST databases and indices on both Tusker and Crane.
-In order to use these resources, the "biodata" module needs to be loaded
-first, <https://hcc-docs.unl.edu/x/L4Hn>. The **$BLAST** variable
-contains** **the following currently available databases:
-
-- **16SMicrobial**
-- **env\_nt**
-- **est**
-- **est\_human**
-- **est\_mouse**
-- **est\_others**
-- **gss**
-- **human\_genomic**
-- **human\_genomic\_transcript**
-- **mouse\_genomic\_transcript**
-- **nr**
-- **nt**
-- **other\_genomic**
-- **refseq\_genomic**
-- **refseq\_rna**
-- **sts**
-- **swissprot**
-- **tsa\_nr**
-- **tsa\_nt**
-
-If you want to create and use a BLAST database that is not mentioned
-above, check [Create Local BLAST
-Database](Create-Local-BLAST-Database_8193290.html).
-
-
-
-Basic SLURM example of nucleotide blast run against the
-non-redundant **nt** BLAST database downloaded on HCC with 8 CPUs is
-provided below.
-When running BLAST alignment, it is recommended to first copy the query
-and database files to the *scratch/* directory on the worker node.
-Moreover, the blast output is also saved in this directory
-(*/scratch/blastn\_output.alignments*). After BLAST finishes, the output
-file is copied from the worker node to your current work directory on
-the login node.
-
-**Please note that the worker nodes can not write to the */home*
-directories and therefore you need to run your job from your */work*
-directory.**
-
-**blastn\_alignment.submit**
-
-\#!/bin/sh
-\#SBATCH --job-name=BlastN
-\#SBATCH --nodes=1
-\#SBATCH --ntasks-per-node=8
-\#SBATCH --time=168:00:00
-\#SBATCH --mem=20gb
-\#SBATCH --output=BlastN.%J.out
-\#SBATCH --error=BlastN.%J.err
-
-
-module load biodata/1.0
+{{< highlight bash >}}
+$ blastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options]
+{{< /highlight >}}
+where **input_reads.fasta** is an input file of sequence data in fasta format, **input_reads_db** is the generated BLAST database, and **blastn_output.alignments** is the output file where the alignments are stored.
+
+Additional parameters can be found in the [BLAST manual] (https://www.ncbi.nlm.nih.gov/books/NBK279690/), or by typing:
+{{< highlight bash >}}
+$ blastn -help
+{{< /highlight >}}
+
+These BLAST alignment commands are multi-threaded, and therefore using the BLAST option **-num_threads <number_of_CPUs>** is recommended.
+
+\\
+HCC hosts multiple BLAST databases and indices on both Tusker and Crane. In order to use these resources, the ["biodata" module] (../../../biodata_module) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:
+
+- **16SMicrobial**
+- **env_nt**
+- **est**
+- **est_human**
+- **est_mouse**
+- **est_others**
+- **gss**
+- **human_genomic**
+- **human_genomic_transcript**
+- **mouse_genomic_transcript**
+- **nr**
+- **nt**
+- **other_genomic**
+- **refseq_genomic**
+- **refseq_rna**
+- **sts**
+- **swissprot**
+- **tsa_nr**
+- **tsa_nt**
+
+If you want to create and use a BLAST database that is not mentioned above, check [Create Local BLAST Database](create_local_blast_database).
+
+\\
+Basic SLURM example of nucleotide BLAST run against the non-redundant **nt** BLAST database with `8 CPUs` is provided below. When running BLAST alignment, it is recommended to first copy the query and database files to the **/scratch/** directory of the worker node. Moreover, the BLAST output is also saved in this directory (**/scratch/blastn_output.alignments**). After BLAST finishes, the output file is copied from the worker node to your current work directory.
+{{% notice info %}}
+**Please note that the worker nodes can not write to the */home/* directories and therefore you need to run your job from your */work/* directory.**
+{{% /notice %}}
+
+{{% panel header="`blastn_alignment.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=BlastN
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+#SBATCH --time=168:00:00
+#SBATCH --mem=20gb
+#SBATCH --output=BlastN.%J.out
+#SBATCH --error=BlastN.%J.err
module load blast/2.7
-
-cd $WORK/<project\_folder>
-
-cp $BLAST/nt.\* /scratch/
-cp <span style="line-height: 1.4285715;">input\_reads.fasta</span>
-/scratch/
-
-blastn -query /scratch/input\_reads.fasta -db /scratch/nt -out
-/scratch/blastn\_output.alignments -num\_threads
-$SLURM\_NTASKS\_PER\_NODE
-
-cp /scratch/blastn\_output.alignments $WORK/<project\_folder>
-
-
-
-One important BLAST parameter is the **e-value threshold** that changes
-the number of hits returned by showing only those with value lower than
-the given. To show the hits with **e-value** lower than 1e-10, modify
-the given script as follows:
-
-**BLASTN with E-value Option**
-
-``` syntaxhighlighter-pre
-blastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignments -num_threads $SLURM_NTASKS_PER_NODE -evalue 1e-10
-```
-
-The default BLAST output is in pairwise format. However, BLAST’s
-parameter **-outfmt** supports output in different formats that are
-easier for parsing
-(<a href="https://www.ncbi.nlm.nih.gov/books/NBK279675/" class="external-link">https://www.ncbi.nlm.nih.gov/books/NBK279675/</a>).
-
-
-
-Basic SLURM example of protein blast run against the
-non-redundant **nr **BLAST database downloaded on HCC with tabular
-output format and 8 CPUs is shown below.
-The query and database files are copied to the *scratch/* directory. The
-blast output is also saved in this directory
-(*/scratch/blastx\_output.alignments*). After BLAST finishes, the output
-file is copied from the worker node to your current work directory on
-the login node.
-
-**Please note that the worker nodes can not write to
-the */home* directories and therefore you need to run your job from
-the */work* directory.**
-
-**blastx\_alignment.submit**
-
-\#!/bin/sh
-\#SBATCH --job-name=BlastX
-\#SBATCH --nodes=1
-\#SBATCH --ntasks-per-node=8
-\#SBATCH --time=168:00:00
-\#SBATCH --mem=20gb
-\#SBATCH --output=BlastX.%J.out
-\#SBATCH --error=BlastX.%J.err
-
-
-
module load biodata/1.0
-module load blast/2.7
-
-cd $WORK/<project\_folder>
+cd $WORK/<project_folder>
+cp $BLAST/nt.* /scratch/
+cp input_reads.fasta /scratch/
+
+blastn -query /scratch/input_reads.fasta -db /scratch/nt -out /scratch/blastn_output.alignments -num_threads $SLURM_NTASKS_PER_NODE
+
+cp /scratch/blastn_output.alignments $WORK/<project_folder>
+{{< /highlight >}}
+{{% /panel %}}
+
+\\
+One important BLAST parameter is the **e-value threshold** that changes the number of hits returned by showing only those with value lower than the given. To show the hits with **e-value** lower than 1e-10, modify the given script as follows:
+{{< highlight bash >}}
+$ blastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignments -num_threads $SLURM_NTASKS_PER_NODE -evalue 1e-10
+{{< /highlight >}}
+
+\\
+The default BLAST output is in pairwise format. However, BLAST’s parameter **-outfmt** supports output in [different formats] (https://www.ncbi.nlm.nih.gov/books/NBK279684/) that are easier for parsing.
+
+\\
+Basic SLURM example of protein BLAST run against the non-redundant **nr **BLAST database with tabular output format and `8 CPUs` is shown below. Similarly as before, the query and database files are copied to the **/scratch/** directory. The BLAST output is also saved in this directory (**/scratch/blastx_output.alignments**). After BLAST finishes, the output file is copied from the worker node to your current work directory.
+{{% notice info %}}
+**Please note that the worker nodes can not write to the */home/* directories and therefore you need to run your job from your */work/* directory.**
+{{% /notice %}}
+
+{{% panel header="`blastx_alignment.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=BlastX
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+#SBATCH --time=168:00:00
+#SBATCH --mem=20gb
+#SBATCH --output=BlastX.%J.out
+#SBATCH --error=BlastX.%J.err
-cp $BLAST/nr.\* /scratch/
-cp input\_reads.fasta /scratch/
-
-blastx -query /scratch/input\_reads.fasta -db /scratch/nr -outfmt 6 -out
-/scratch/blastx\_output.alignments -num\_threads
-$SLURM\_NTASKS\_PER\_NODE
-
-cp /scratch/blastx\_output.alignments $WORK/<project\_folder>
-
-Attachments:
-------------
+module load blast/2.7
+module load biodata/1.0
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_blast\_module.xsl](attachments/8193291/8127544.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193291/8127545.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_blastn\_biodata.xsl](attachments/8193291/16521350.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193291/17039409.xml) (text/xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193291/35326588.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193291/35326639.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193291/35326661.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193291/35326819.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193291/16521353.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193291/35326896.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193291/35326931.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193291/35326950.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193291/35327032.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193291/35325367.xml) (text/xml)
+cd $WORK/<project_folder>
+cp $BLAST/nr.* /scratch/
+cp input_reads.fasta /scratch/
+blastx -query /scratch/input_reads.fasta -db /scratch/nr -outfmt 6 -out /scratch/blastx_output.alignments -num_threads $SLURM_NTASKS_PER_NODE
+cp /scratch/blastx_output.alignments $WORK/<project_folder>
+{{< /highlight >}}
+{{% /panel %}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blat.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blat.md
index 626db318d166d2e314fa6860bd7c44379206fc06..4f18d22a93ac9e2ba87433247aeb26554761ad58 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blat.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blat.md
@@ -1,108 +1,51 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Alignment Tools](Alignment-Tools_8193288.html)
++++
+title = "BLAT"
+description = "How to run BLAT on HCC resources"
+weight = "10"
++++
-<span id="title-text"> HCC-DOCS : BLAT </span>
-==============================================
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
-
-| Name | Version | Resource |
-|------|---------|----------|
-| blat | 35x1 | Tusker |
-
-| | | |
-|------|------|-------|
-| blat | 35x1 | Crane |
-
-<span style="line-height: 1.4285715;">
-</span>
-
-<span style="line-height: 1.4285715;">BLAT is a pairwise alignment tool
-similar to BLAST. It is more accurate and about 500 times faster than
-the existing tools for mRNA/DNA alignments and it is about 50 times
-faster with protein/protein alignments. BLAT accepts short and long
-query and database sequences as input files.</span>
+BLAT is a pairwise alignment tool similar to BLAST. It is more accurate and about 500 times faster than the existing tools for mRNA/DNA alignments and it is about 50 times faster with protein/protein alignments. BLAT accepts short and long query and database sequences as input files.
The basic usage of BLAT is:
-
-**General BLAT Usage**
-
-``` syntaxhighlighter-pre
-blat database query output_alignment.txt [options]
-```
-
-where **database** is the name of the database used for the alignment,
-**query** is the name of the input file of sequence data in
-fasta/nib/2bit format, and **output\_alignment.txt** is the output
-alignment file. Additional parameters for BLAT alignment can be found in
-the
-manual: <a href="http://genome.ucsc.edu/goldenPath/help/blatSpec.html" class="external-link">http://genome.ucsc.edu/goldenPath/help/blatSpec.html</a>,
-or by using
-
-**Additional BLAT Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.tusker~]$ blat
-```
-
-Running BLAT on Tusker with query file **input\_reads.fasta** and
-database **db.fa** is shown below:
-
-**blat\_alignment.submit**
-
-\#!/bin/sh
-\#SBATCH --job-name=Blat
-\#SBATCH --nodes=1
-\#SBATCH --ntasks-per-node=1
-\#SBATCH --time=168:00:00
-\#SBATCH --mem=50gb
-\#SBATCH --output=Blat.%J.out
-\#SBATCH --error=Blat.%J.err
-
-
-
-| |
-|-----------------------|
-| module load blat/35x1 |
-
-blat db.fa input\_reads.fasta output\_alignment.txt
-
-Although BLAT is a single threaded program (**\#SBATCH --nodes=1**,
-**\#SBATCH --ntasks-per-node=1**) it is still much faster than the other
-alignment tools.
-
-
-
-**BLAT Output**
-
-BLAT output is a list containing the following information: *the score
-of the alignment*, *the region of query sequence that matches the
-database sequence*, *the size of the query sequence*, *the level of
-identity as a percentage of the alignment* and *the chromosome and
-position that the query sequence maps to*.
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_blat\_module.xsl](attachments/8193292/8127546.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_blat\_version.xsl](attachments/8193292/8127547.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193292/8127548.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_blat\_version.xsl](attachments/8193292/8127549.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193292/8127550.xml)
-(application/octet-stream)
-
-
+{{< highlight bash >}}
+$ blat database query output_alignment.txt [options]
+{{< /highlight >}}
+where **database** is the name of the database used for the alignment, **query** is the name of the input file of sequence data in `fasta/nib/2bit` format, and **output_alignment.txt** is the output alignment file.
+
+Additional parameters for BLAT alignment can be found in the [manual] (http://genome.ucsc.edu/FAQ/FAQblat), or by using:
+{{< highlight bash >}}
+$ blat
+{{< /highlight >}}
+
+\\
+Running BLAT on Tusker with query file `input_reads.fasta` and database `db.fa` is shown below:
+{{% panel header="`blat_alignment.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=Blat
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=168:00:00
+#SBATCH --mem=50gb
+#SBATCH --output=Blat.%J.out
+#SBATCH --error=Blat.%J.err
+
+module load blat/35x1
+
+blat db.fa input_reads.fasta output_alignment.txt
+{{< /highlight >}}
+{{% /panel %}}
+
+Although BLAT is a single threaded program (`#SBATCH --nodes=1`, `#SBATCH --ntasks-per-node=1`) it is still much faster than the other alignment tools.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BLAT Output</span>
+
+BLAT output is a list containing the following information:
+
+- the score of the alignment
+- the region of query sequence that matches the database sequence
+- the size of the query sequence
+- the level of identity as a percentage of the alignment
+- the chromosome and position that the query sequence maps to
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie.md
index 156855fc8f055569beaf12481fb1a7c35fb93c89..abcef635fb5ad11153298cbf3ed116c59e1357af 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie.md
@@ -1,3287 +1,46 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Alignment Tools](Alignment-Tools_8193288.html)
-
-<span id="title-text"> HCC-DOCS : Bowtie </span>
-================================================
-
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
-
-| Name | Version | Resource |
-|--------|---------|----------|
-| bowtie | 0.12.8 | Tusker |
-| bowtie | 0.12.9 | Tusker |
-| bowtie | 1.0.0 | Tusker |
-| bowtie | 1.1.2 | Tusker |
-
-| | | |
-|--------|-------|-------|
-| bowtie | 1.0 | Crane |
-| bowtie | 1.1.2 | Crane |
-
-
-
-Bowtie
-(<a href="http://bowtie-bio.sourceforge.net/index.shtml" class="external-link">http://bowtie-bio.sourceforge.net/index.shtml</a>)
-is an ultrafast and memory-efficient aligner for large sets of
-sequencing reads to a reference genome. Bowtie indexes the genome with a
-Burrows-Wheeler index to keep its memory footprint small. Bowtie also
-supports usage of multiple processors to achieve greater alignment
-speed.
-
-The first and basic step of running Bowtie is to build and format an
-index from the reference genome. The basic usage of this command
-**bowtie-build** is:
-
-**General Bowtie-Build Usage**
-
-``` syntaxhighlighter-pre
-bowtie-build input_reference.fasta index_prefix
-```
-
-where **input\_reference.fasta** is an input file of sequence reads in
-fasta format, and **index\_prefix** is the prefix of the generated index
-files.
-
-After the index of the reference genome is generated, the next step is
-to align the reads. The basic usage of bowtie is:
-
-**General Bowtie Usage**
-
-``` syntaxhighlighter-pre
-bowtie [-q|-f|-r|-c] index_prefix [-1 input_reads_pair_1.[fasta|fastq] -2 input_reads_pair_2.[fasta|fastq] | input_reads.[fasta|fastq]] [options]
-```
-
-where **index\_prefix** is the generated index using the
-**bowtie-build** command, and **options** are optional parameters that
-can be found in the Bowtie
-manual: <a href="http://bowtie-bio.sourceforge.net/manual.shtml" class="external-link">http://bowtie-bio.sourceforge.net/manual.shtml</a>.
-Bowtie supports both single-end (**input\_reads.\[fasta\|fastq\]**) and
-paired-end
-(i**nput\_reads\_pair\_1.\[fasta\|fastq\]**, **input\_reads\_pair\_2.\[fasta\|fastq\]**)
-files in fasta or fastq format. The format of the input files also needs
-to be specified by using the following flags: **-q** (fastq files),
-**-f** (fasta files), **-r**(raw one-sequence per line), or **-c**
-(sequences given on command line).
-
-An example of how to run Bowtie alignment on Tusker with single-end
-fastq file and 8 CPUs is shown below:
-
-**bowtie\_alignment.submit**
-
-\#!/bin/sh
-\#SBATCH --job-name=Bowtie
-\#SBATCH --nodes=1
-\#SBATCH --ntasks-per-node=8
-\#SBATCH --time=168:00:00
-\#SBATCH --mem=50gb
-\#SBATCH --output=Bowtie.%J.out
-\#SBATCH --error=Bowtie.%J.err
-
-
-
-| |
-|------------------------|
-| module load bowtie/1.1 |
-
-bowtie -q index\_prefix input\_reads.fastq -p $SLURM\_NTASKS\_PER\_NODE
-> bowtie\_alignments.sam
-
-
-
-**Bowtie Output**
-
-Bowtie output is an alignment file in SAM format, where one line is one
-alignment. Each line is a collection of 8 fields separated by tabs. The
-fields are: *name of the aligned reads*, r*eference strand aligned to*,
-*name of reference sequence where the alignment occurs*, *0-based offset
-into the forward reference strand where leftmost character of the
-alignment occurs*, *read sequence*, *read qualities*, *the number of
-other instances where the same sequence is aligned against the same
-reference characters*, and *comma-separated list of mismatch
-descriptors*.
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_bowtie\_module.xsl](attachments/8193293/8127551.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_bowtie\_version.xsl](attachments/8193293/8127552.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_bowtie\_version.xsl](attachments/8193293/8127554.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193293/11637641.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/11637449.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/11637481.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/11637513.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/11637550.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/11637598.xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/11637720.xml)
-(application/octet-stream)
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-[tusker\_modules.xml](attachments/8193293/11637925.xml)
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-[crane\_modules.xml](attachments/8193293/11637747.xml)
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-[crane\_modules.xml](attachments/8193293/11637856.xml)
-(application/octet-stream)
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-[crane\_modules.xml](attachments/8193293/11638118.xml)
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-[tusker\_modules.xml](attachments/8193293/11638161.xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/11638231.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193293/11638204.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193293/12550247.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/12386337.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/13041702.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193293/12550295.xml)
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-[tusker\_modules.xml](attachments/8193293/12550345.xml)
-(application/octet-stream)
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-[tusker\_modules.xml](attachments/8193293/13041756.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/13041800.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193293/13041844.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/13041873.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193293/13041916.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/13042008.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193293/13041978.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193293/13042134.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/13042037.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193293/13042064.xml)
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-[crane\_modules.xml](attachments/8193293/13042215.xml)
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-[crane\_modules.xml](attachments/8193293/13042382.xml)
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-[tusker\_modules.xml](attachments/8193293/13042307.xml)
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-[tusker\_modules.xml](attachments/8193293/13042350.xml)
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-[tusker\_modules.xml](attachments/8193293/13042453.xml)
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-[crane\_modules.xml](attachments/8193293/13042409.xml)
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-[crane\_modules.xml](attachments/8193293/13042480.xml)
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-[tusker\_modules.xml](attachments/8193293/13042523.xml)
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-[crane\_modules.xml](attachments/8193293/13042550.xml)
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-[tusker\_modules.xml](attachments/8193293/13042620.xml)
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-[crane\_modules.xml](attachments/8193293/13042577.xml)
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-[crane\_modules.xml](attachments/8193293/13042693.xml)
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-[tusker\_modules.xml](attachments/8193293/13599012.xml)
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-[crane\_modules.xml](attachments/8193293/13598969.xml)
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-[crane\_modules.xml](attachments/8193293/13599148.xml)
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-[tusker\_modules.xml](attachments/8193293/33689784.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193293/33690004.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193293/35324884.xml)
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-[tusker\_modules.xml](attachments/8193293/35325646.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193293/35325227.xml) (text/xml)
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-(application/octet-stream)
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-[crane\_modules.xml](attachments/8193293/35325270.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193293/35325574.xml)
-(application/octet-stream)
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-[crane\_modules.xml](attachments/8193293/35325577.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193293/35325691.xml)
-(application/octet-stream)
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-(application/octet-stream)
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-[tusker\_modules.xml](attachments/8193293/35325759.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193293/35326152.xml)
-(application/octet-stream)
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-[crane\_modules.xml](attachments/8193293/35326155.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193293/35326716.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193293/35326746.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193293/35326678.xml)
-(application/octet-stream)
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-[crane\_modules.xml](attachments/8193293/35326681.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193293/11637420.xml)
-(application/octet-stream)
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-[crane\_modules.xml](attachments/8193293/17044367.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193293/11637419.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193293/17044366.xml) (text/xml)
-
-
++++
+title = "Bowtie"
+description = "How to run Bowtie on HCC resources"
+weight = "10"
++++
+
+[Bowtie] (http://bowtie-bio.sourceforge.net/index.shtml) is an ultrafast and memory-efficient aligner for large sets of sequencing reads to a reference genome. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small. Bowtie also supports usage of multiple processors to achieve greater alignment speed.
+
+The first and basic step of running Bowtie is to build and format an index from the reference genome. The basic usage of this command, **bowtie-build** is:
+{{< highlight bash >}}
+$ bowtie-build input_reference.fasta index_prefix
+{{< /highlight >}}
+where **input_reference.fasta** is an input file of sequence reads in fasta format, and **index_prefix** is the prefix of the generated index files.
+
+After the index of the reference genome is generated, the next step is to align the reads. The basic usage of bowtie is:
+{{< highlight bash >}}
+$ bowtie [-q|-f|-r|-c] index_prefix [-1 input_reads_pair_1.[fasta|fastq] -2 input_reads_pair_2.[fasta|fastq] | input_reads.[fasta|fastq]] [options]
+{{< /highlight >}}
+where **index_prefix** is the generated index using the **bowtie-build** command, and **options** are optional parameters that can be found in the [Bowtie
+manual] (http://bowtie-bio.sourceforge.net/manual.shtml).
+
+Bowtie supports both single-end (`input_reads.[fasta|fastq]`) and paired-end (`input_reads_pair_1.[fasta|fastq]`, `input_reads_pair_2.[fasta|fastq]`) files in fasta or fastq format. The format of the input files also needs to be specified by using the following flags: **-q** (fastq files), **-f** (fasta files), **-r** (raw one-sequence per line), or **-c** (sequences given on command line).
+
+\\
+An example of how to run Bowtie alignment on Tusker with single-end fastq file and `8 CPUs` is shown below:
+{{% panel header="`bowtie_alignment.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=Bowtie
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=Bowtie.%J.out
+#SBATCH --error=Bowtie.%J.err
+
+module load bowtie/1.1
+
+bowtie -q index_prefix input_reads.fastq -p $SLURM_NTASKS_PER_NODE > bowtie_alignments.sam
+{{< /highlight >}}
+{{% /panel %}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Bowtie Output</span>
+
+Bowtie output is an alignment file in SAM format, where one line is one alignment. Each line is a collection of 8 fields separated by tabs. The fields are: name of the aligned reads, reference strand aligned to, name of reference sequence where the alignment occurs, 0-based offset into the forward reference strand where leftmost character of the alignment occurs, read sequence, read qualities, the number of other instances where the same sequence is aligned against the same reference characters, and comma-separated list of mismatch descriptors.
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie2.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie2.md
index 8ba4fb1b6226d3be8e4e57f2a687c0a94b100ea2..b92784fc77d28a1b2ef771f444feffd949f9e61f 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie2.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bowtie2.md
@@ -1,952 +1,52 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Alignment Tools](Alignment-Tools_8193288.html)
-
-<span id="title-text"> HCC-DOCS : Bowtie2 </span>
-=================================================
-
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
-
-| Name | Version | Resource |
-|--------|-------------|----------|
-| bowtie | 2.0.0-beta6 | Tusker |
-| bowtie | 2.1.0 | Tusker |
-| bowtie | 2.2.6 | Tusker |
-| bowtie | 2.3.4 | Tusker |
-
-| | | |
-|--------|-------|-------|
-| bowtie | 2.2.6 | Crane |
-| bowtie | 2.3.4 | Crane |
-
-
-
-Bowtie2
-(<a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml" class="external-link">http://bowtie-bio.sourceforge.net/bowtie2/index.shtml</a>)
-is an ultrafast and memory-efficient tool for aligning sequencing reads
-to long reference sequences. Although Bowtie and Bowtie2 are both fast
-read aligners, there are few main differences between them:
-
-- Bowtie2 supports gapped alignment with affine gap penalties, without
- restrictions on the number of gaps and gap lengths.
-- Bowtie supports reads longer than 50bp and is generally faster, more
- sensitive, and uses less memory than Bowtie.
-- Bowtie support only end-to-end alignments, while Bowtie2 supports
- both end-to-end and local alignment.
-- Bowtie has an upper limit on read length of around 1,000 bp, while
- Bowtie2 does not have any.
-- Bowtie2's paired-end alignment is more flexible that Bowtie's.
-- Bowtie2 does not align colorspace reads.
-- Bowtie and Bowtie2 indices are not compatible.
-
-Same as Bowtie, the first and basic step of running Bowtie2 is to build
-a Bowtie2 index from a reference genome sequence. The basic usage of the
-command **bowtie2-build** is:
-
-**General Bowtie2-Build Usage**
-
-``` syntaxhighlighter-pre
-bowtie2-build -f input_reference.fasta index_prefix
-```
-
-where **input\_reference.fasta** is an input file of sequence reads in
-fasta format, and **index\_prefix** is the prefix of the generated index
-files. Beside the option **-f** that is used when the reference input
-file is a fasta file, the option **-c** can be used when the reference
-sequences are given on the command line.
-
-The command **bowtie2** takes a Bowtie2 index and set of sequencing read
-files and outputs set of alignments in SAM format. The general
-**bowtie2** usage is:
-
-**General Bowtie2 Usage**
-
-``` syntaxhighlighter-pre
-bowtie2 -x index_prefix [-q|--qseq|-f|-r|-c] [-1 input_reads_pair_1.[fasta|fastq] -2 input_reads_pair_2.[fasta|fastq] | -U input_reads.[fasta|fastq]] -S bowtie2_alignments.sam [options]
-```
-
-where **index\_prefix** is the generated index using
-the **bowtie2-build** command, and **options** are optional parameters
-that can be found in the Bowtie2
-manual: <a href="http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml" class="external-link">http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml</a>. Bowtie2
-supports both single-end (**input\_reads.\[fasta\|fastq\]**) and
-paired-end
-(i**nput\_reads\_pair\_1.\[fasta\|fastq\]**, **input\_reads\_pair\_2.\[fasta\|fastq\]**)
-files in fasta or fastq format. The format of the input files also needs
-to be specified by using one of the following flags: **-q** (fastq
-files), **--qseq** (Illumina's qseq format), **-f** (fasta files),
-**-r** (raw one sequence per line), or **-c** (sequences given on
-command line).
-
-An example of how to run Bowtie2 local alignment on Tusker with
-paired-end fasta files and 8 CPUs is shown below:
-
-**bowtie2\_alignment.submit**
-
-\#!/bin/sh
-\#SBATCH --job-name=Bowtie2
-\#SBATCH --nodes=1
-\#SBATCH --ntasks-per-node=8
-\#SBATCH --time=168:00:00
-\#SBATCH --mem=50gb
-\#SBATCH --output=Bowtie2.%J.out
-\#SBATCH --error=Bowtie2.%J.err
-
-
-
-| |
-|------------------------|
-| module load bowtie/2.3 |
-
-bowtie2 -x index\_prefix -f -1 input\_reads\_pair\_1.fasta -2
-input\_reads\_pair\_2.fasta -S bowtie2\_alignments.sam --local -p
-$SLURM\_NTASKS\_PER\_NODE
-
-
-
-**Bowtie2 Output**
-
-Bowtie2 outputs alignments in SAM format that can further be manipulated
-with different tools, like SAMtools and GATK. Each line from the file
-describes an alignment and is a collection of at least 12 fields
-separated by tabs. Detailed information about Bowtie2 output fields can
-be found in the Bowtie2 manual.
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_bowtie2\_module.xsl](attachments/8193294/8127556.xsl)
-(application/octet-stream)
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-[crane\_modules.xml](attachments/8193294/18546913.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193294/18547016.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193294/18547272.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193294/18547409.xml) (text/xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30446464.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30446586.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30446507.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30446549.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30446745.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30446645.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30446822.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30446787.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30446889.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30446924.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30447051.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30447086.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30447222.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30447148.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30447257.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30447322.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30447481.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30447363.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30447404.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30447445.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30447550.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30447585.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30447723.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30447658.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30447758.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30447823.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30447993.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30447900.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30447958.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30448058.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30448093.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30448407.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30448299.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30448442.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30448537.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30448669.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30448583.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30448634.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30448737.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30448772.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30448844.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30448879.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/30448952.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/30448987.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/33685577.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/33685608.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/33685688.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/33685719.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/33685800.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/33685831.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/33685905.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/33685936.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/33686042.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/33686073.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/33686146.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/33686177.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/33686285.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/33686316.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/33687821.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/33687852.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/33688427.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/33688461.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/33689754.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/33689785.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/33689974.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/33690005.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/35323983.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/35324045.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/35324093.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/35324155.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/35324431.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/35324625.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/35324561.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/35324851.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/35324915.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/35325016.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/35325647.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/35325185.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/35325228.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/35325271.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/35325578.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/35325695.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/35325760.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/35326156.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/35326747.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/35326682.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193294/17044368.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193294/17044369.xml) (text/xml)
-
-
++++
+title = "Bowtie2"
+description = "How to run Bowtie2 on HCC resources"
+weight = "10"
++++
+
+[Bowtie2] (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. Although Bowtie and Bowtie2 are both fast read aligners, there are few main differences between them:
+
+- Bowtie2 supports gapped alignment with affine gap penalties, without restrictions on the number of gaps and gap lengths.
+- Bowtie supports reads longer than 50bp and is generally faster, more sensitive, and uses less memory than Bowtie.
+- Bowtie support only end-to-end alignments, while Bowtie2 supports both end-to-end and local alignment.
+- Bowtie has an upper limit on read length of around 1,000 bp, while Bowtie2 does not have any.
+- Bowtie2's paired-end alignment is more flexible that Bowtie's.
+- Bowtie2 does not align colorspace reads.
+- Bowtie and Bowtie2 indices are not compatible.
+
+Same as Bowtie, the first and basic step of running Bowtie2 is to build Bowtie2 index from a reference genome sequence. The basic usage of the
+command **bowtie2-build** is:
+{{< highlight bash >}}
+$ bowtie2-build -f input_reference.fasta index_prefix
+{{< /highlight >}}
+where **input_reference.fasta** is an input file of sequence reads in fasta format, and **index_prefix** is the prefix of the generated index files. Beside the option **-f** that is used when the reference input file is a fasta file, the option **-c** can be used when the reference sequences are given on the command line.
+
+The command **bowtie2** takes a Bowtie2 index and set of sequencing read files and outputs set of alignments in SAM format. The general **bowtie2** usage is:
+{{< highlight bash >}}
+$ bowtie2 -x index_prefix [-q|--qseq|-f|-r|-c] [-1 input_reads_pair_1.[fasta|fastq] -2 input_reads_pair_2.[fasta|fastq] | -U input_reads.[fasta|fastq]] -S bowtie2_alignments.sam [options]
+{{< /highlight >}}
+where **index_prefix** is the generated index using the **bowtie2-build** command, and **options** are optional parameters that can be found in the [Bowtie2 manual] (http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml). Bowtie2 supports both single-end (`input_reads.[fasta|fastq]`) and paired-end (`input_reads_pair_1.[fasta|fastq]`, `input_reads_pair_2.[fasta|fastq]`) files in fasta or fastq format. The format of the input files also needs to be specified by using one of the following flags: **-q** (fastq files), **--qseq** (Illumina's qseq format), **-f** (fasta files), **-r** (raw one sequence per line), or **-c** (sequences given on command line).
+
+\\
+An example of how to run Bowtie2 local alignment on Tusker with paired-end fasta files and `8 CPUs` is shown below:
+{{% panel header="`bowtie2_alignment.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=Bowtie2
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=Bowtie2.%J.out
+#SBATCH --error=Bowtie2.%J.err
+
+module load bowtie/2.3
+
+bowtie2 -x index_prefix -f -1 input_reads_pair_1.fasta -2 input_reads_pair_2.fasta -S bowtie2_alignments.sam --local -p $SLURM_NTASKS_PER_NODE
+{{< /highlight >}}
+{{% /panel %}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Bowtie2 Output</span>
+
+Bowtie2 outputs alignments in SAM format that can further be manipulated with different tools, like SAMtools and GATK. Each line from the file describes an alignment and is a collection of at least 12 fields separated by tabs. Detailed information about Bowtie2 output fields can be found in the Bowtie2 manual.
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
index 6c279db3da7d6e69cabce46d43c047bbbd76513e..53e855a35dfb63f2ba0f299705f8d7a922df43f3 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
@@ -1,904 +1,38 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Alignment Tools](Alignment-Tools_8193288.html)
-
-<span id="title-text"> HCC-DOCS : BWA </span>
-=============================================
-
-Created by <span class="author"> Adam Caprez</span> on Sep 04, 2014
-
-| Name | Version | Resource |
-|------|---------|----------|
-| bwa | 0.6.2 | Tusker |
-| bwa | 0.7 | Tusker |
-
-| | | |
-|-----|-------|-------|
-| bwa | 0.6.2 | Crane |
-| bwa | 0.7 | Crane |
-
++++
+title = "BWA"
+description = "How to use BWA on HCC machines"
+weight = "52"
++++
-BWA (Burrows-Wheeler Aligner) is a software package for mapping
-relatively short nucleotide sequences against a long reference
-sequence. BWA is slower than Bowtie, but allows indels in the alignment.
+BWA (Burrows-Wheeler Aligner) is a software package for mapping relatively short nucleotide sequences against a long reference sequence. BWA is slower than Bowtie, but allows indels in the alignment.
The basic usage of BWA is:
-
-**General BWA Usage**
-
-``` syntaxhighlighter-pre
-bwa COMMAND [options]
-```
-
-where **COMMAND** is one of the available BWA commands**:**
-
-- **index**: index sequences in the FASTA format
-- **mem**: BWA-MEM algorithm
-- **fastmap**: identify super-maximal exact matches
-- **pemerge**: merge overlapping paired ends (EXPERIMENTAL)
-- **aln**: gapped/ungapped alignment
-- **samse**: generate alignment (single ended)
-- **sampe**: generate alignment (paired ended)
-- **bwasw**: BWA-SW for long queries
-- **fa2pac**: convert FASTA to PAC format
-- **pac2bwt**: generate BWT from PAC
-- **pac2bwtgen**: alternative algorithm for generating BWT
-- **bwtupdate**: update .bwt to the new format
-- **bwt2sa**: generate SA from BWT and Occ
-
-BWA supports three alignment algorithms: **mem**, **bwasw**, and
-**aln**/**samse**/**sampe**. **BWA mem** is the latest algorithm, and is
-faster, more accurate and has better performance than **BWA bwasw** and
-**BWA aln**/**samse**/**sampe**. Therefore, if there are not any
-specific reasons, **BWA mem** is recommended for first-time users.
-
-For detailed description and more information on a specific command,
-just type:
-
-**General BWA COMMAND Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.tusker~]$ bwa COMMAND
-```
-
-or check the BWA
-manual: <a href="http://bio-bwa.sourceforge.net/bwa.shtml" class="external-link">http://bio-bwa.sourceforge.net/bwa.shtml</a>.
-
-The page [Running BWA Commands](Running-BWA-Commands_8193296.html) shows
-how to run BWA on HCC.
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_bwa\_version.xsl](attachments/8193295/8127561.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193295/8127562.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_bwa\_version.xsl](attachments/8193295/8127563.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193295/8127564.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193295/17044384.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193295/17044421.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193295/17044488.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193295/17044525.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193295/17044584.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193295/17044621.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193295/17044681.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193295/33689975.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193295/33690007.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193295/35323984.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193295/35324047.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193295/35324094.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193295/35324157.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193295/35324432.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193295/35324627.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193295/35324562.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193295/35325186.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193295/35326157.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193295/35326749.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193295/35326683.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193295/17044370.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193295/17044371.xml) (text/xml)
-
-
+{{< highlight bash >}}
+$ bwa COMMAND [options]
+{{< /highlight >}}
+where **COMMAND** is one of the available BWA commands:
+
+- **index**: index sequences in the FASTA format
+- **mem**: BWA-MEM algorithm
+- **fastmap**: identify super-maximal exact matches
+- **pemerge**: merge overlapping paired ends (EXPERIMENTAL)
+- **aln**: gapped/ungapped alignment
+- **samse**: generate alignment (single ended)
+- **sampe**: generate alignment (paired ended)
+- **bwasw**: BWA-SW for long queries
+- **fa2pac**: convert FASTA to PAC format
+- **pac2bwt**: generate BWT from PAC
+- **pac2bwtgen**: alternative algorithm for generating BWT
+- **bwtupdate**: update .bwt to the new format
+- **bwt2sa**: generate SA from BWT and Occ
+
+BWA supports three alignment algorithms, **mem**, **bwasw**, and **aln**/**samse**/**sampe**. **bwa mem** is the latest algorithm, and is faster, more accurate and has better performance than **bwa bwasw** and **bwa aln**/**samse**/**sampe**. Therefore, if there are not any specific reasons, **bwa mem** is recommended for first-time users.
+
+For detailed description and more information on a specific command, just type:
+{{< highlight bash >}}
+$ bwa COMMAND
+{{< /highlight >}}
+or check the [BWA manual] (http://bio-bwa.sourceforge.net/bwa.shtml).
+
+The page [Running BWA Commands](running_bwa_commands) shows how to run BWA on HCC.
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md
index beec63f485922f6c84a5fc9c8c3985482663c839..f7f274ad7a7caf0e6ce6149386c04a3c6dced846 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands.md
@@ -1,320 +1,141 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Alignment Tools](Alignment-Tools_8193288.html)
-7. [BWA](BWA_8193295.html)
++++
+title = "Running BWA Commands"
+description = "How to run BWA commands on HCC resources"
+weight = "10"
++++
+
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BWA Index:</span>
+
+The first step of using BWA is to make an index of the reference genome in fasta format. The basic usage of the **bwa index** is:
+{{< highlight bash >}}
+$ bwa index [-a bwtsw|is] input_reference.fasta index_prefix
+{{< /highlight >}}
+where **input_reference.fasta** is an input file of the reference genome in fasta format, and **index_prefix** is the prefix of the generated index files. The option **-a** is required and can have two values: **bwtsw** (does not work for short genomes) and **is** (does not work for long genomes). Therefore, this value is chosen according to the length of the genome.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BWA Mem:</span>
+
+The **bwa mem** algorithm is one of the three algorithms provided by BWA. It performs local alignment and produces alignments for different part of the query sequence. The basic usage of **bwa mem** is:
+{{< highlight bash >}}
+$ bwa mem index_prefix [input_reads.fastq|input_reads_pair_1.fastq input_reads_pair_2.fastq] [options]
+{{< /highlight >}}
+where **index_prefix** is the index for the reference genome generated from **bwa index**, and **input_reads.fastq**, **input_reads_pair_1.fastq**, **input_reads_pair_2.fastq** are the input files of sequencing data that can be single-end or paired-end respectively. Additional **options** for **bwa mem** can be found in the BWA manual.
+
+\\
+Simple SLURM script for running **bwa mem** on Tusker with paired-end fastq input data, `index_prefix` as reference genome index, SAM output file and `8 CPUs` is shown below:
+{{% panel header="`bwa_mem.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=Bwa_Mem
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=BwaMem.%J.out
+#SBATCH --error=BwaMem.%J.err
+
+module load bwa/0.7
+
+bwa mem index_prefix input_reads_pair_1.fastq input_reads_pair_2.fastq -t $SLURM_NTASKS_PER_NODE > bwa_mem_alignments.sam
+{{< /highlight >}}
+{{% /panel %}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BWA Bwasw:</span>
+
+The **bwa bwasw** algorithm is another algorithm provided by BWA. For input files with single-end reads it aligns the query sequences. For input files with paired-ends reads it performs paired-end alignment that only works for Illumina reads.
+
+An example of **bwa bwasw** for single-end input file `input-reads.fasta` in fasta format and output file `bwa_bwasw_alignments.sam` where the alignments are stored, is shown below:
+{{< highlight bash >}}
+$ bwa bwasw index_prefix input_reads.fasta -t $SLURM_NTASKS_PER_NODE > bwa_bwasw_alignments.sam
+{{< /highlight >}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BWA Aln:</span>
+
+The third BWA algorithm, **bwa aln**, aligns the input file of sequence data to the reference genome. In addition, there is an example of running **bwa aln** with single-end `input_reads.fasta` input file and `8 CPUs`:
+{{< highlight bash >}}
+$ bwa aln index_prefix input_reads.fasta -0 -t $SLURM_NTASKS_PER_NODE > bwa_aln_alignments.sai
+{{< /highlight >}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BWA Samse and BWA Sampe:</span>
+
+The command **bwa samse** uses the `bwa_aln_alignments.sai` output from **bwa aln** in order to generate SAM file from the alignments for single-end reads.
+
+{{% panel header="`General BWA Samse Usage`"%}}
+{{< highlight bash >}}
+$ bwa samse -f bwa_aln_alignments.sam index_prefix bwa_aln_alignments.sai input_reads.fasta output31.preArc
+{{< /highlight >}}
+{{% /panel %}}
+
+The command **bwa sampe** uses the `bwa_aln_alignments.sai` output form **bwa aln** in order to generate SAM file from the alignments for paired-end reads.
+
+{{% panel header="`General BWA Sampe Usage`"%}}
+{{< highlight bash >}}
+$ bwa samse -f bwa_aln_alignments.sam index_prefix bwa_aln_alignments_pair_1.sai bwa_aln_alignments_pair_2.sai input_reads_pair_1.fasta input_reads_pair_2.fasta
+{{< /highlight >}}
+{{% /panel %}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BWA Fastmap:</span>
+
+The command **bwa fastmap** identifies and outputs super-maximal exact matches (SMEMs). The basic usage of **bwa fastmap** is:
+{{< highlight bash >}}
+$ bwa fastmap index_prefix input_reads.fasta > bwa_fastmap.matches
+{{< /highlight >}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BWA Pemerge:</span>
+
+The command **bwa pemerge** merges overlapping paired ends and can print either only the merged reads or the unmerged ones. An example of **bwa pemerge** of `input_reads_pair_1.fastq` and `input_reads_pair_2.fastq` with `8 CPUs` and output file `output_reads_merged.fastq` that contains only the merged reads is shown below:
+{{< highlight bash >}}
+$ bwa pemerge -m input_reads_pair_1.fastq input_reads_pair_2.fastq -t $SLURM_NTASKS_PER_NODE > output_reads_merged.fastq
+{{< /highlight >}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BWA Fa2pac:</span>
+
+The command **bwa fa2pac** converts fasta to pac files. The general usage of **bwa fa2pac** is:
+{{< highlight bash >}}
+$ bwa fa2pac input_reads.fasta pac_prefix
+{{< /highlight >}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BWA Pac2bwt and BWA Pac2bwtgen:</span>
+
+The commands **bwa pac2bwt** and **bwa pac2bwtgen** convert pac to bwt files.
+
+{{% panel header="`General BWA Pac2bwt Usage`"%}}
+{{< highlight bash >}}
+$ bwa pac2bwt input_reads.pac output_reads.bwt
+{{< /highlight >}}
+{{% /panel %}}
+
+{{% panel header="`General BWA Pac2bwtgen Usage`"%}}
+{{< highlight bash >}}
+$ bwa pac2bwtgen input_reads.pac output_reads.bwt
+{{< /highlight >}}
+{{% /panel %}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BWA Bwtupdate:</span>
-<span id="title-text"> HCC-DOCS : Running BWA Commands </span>
-==============================================================
+The command **bwa bwtupdate** updates bwt files to the new format. The general usage of **bwa bwtupdate** is:
+{{< highlight bash >}}
+$ bwa bwtupdate input_reads.bwt
+{{< /highlight >}}
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BWA Bwt2sa:</span>
-**BWA Index:**
-
-The first step of using BWA is to make an index of the reference genome
-in fasta format. The basic usage of the **bwa index** is:
-
-**General BWA Index Usage**
-
-``` syntaxhighlighter-pre
-bwa index [-a bwtsw|is] input_reference.fasta index_prefix
-```
-
-where **input\_reference.fasta** is an input file of the reference
-genome in fasta format, and **index\_prefix** is the prefix of the
-generated index files. The option **-a** is required and can have two
-values: **bwtsw** (does not work for short genomes) and **is** (does not
-work for long genomes). Therefore, this value is chosen according to the
-length of the genome.
-
-**
-**
-
-**BWA Mem:**
-
-The **bwa mem** algorithm is one of the three algorithms provided by
-BWA. It performs local alignment and produces alignments for different
-part of the query sequence.
-
-**General BWA Mem Usage**
-
-``` syntaxhighlighter-pre
-bwa mem index_prefix [input_reads.fastq|input_reads_pair_1.fastq input_reads_pair_2.fastq] [options]
-```
-
-where **index\_prefix** is the index for the reference genome generated
-from **bwa index**, and **input\_reads.fastq**,
-**input\_reads\_pair\_1.fastq**, **input\_reads\_pair\_2.fastq** are the
-input files of sequencing data that can be single-end or paired-end
-respectively. Additional **options** for **bwa mem** can be found in the
-BWA manual.
-
-Simple SLURM script for running **bwa mem** on Tusker with paired-end
-fastq input data, **index\_prefix** as reference genome index, SAM
-output file and 8 CPUs is shown below:
-
-**bwa\_mem.submit**
-
-\#!/bin/sh
-\#SBATCH --job-name=Bwa\_Mem
-\#SBATCH --nodes=1
-\#SBATCH --ntasks-per-node=8
-\#SBATCH --time=168:00:00
-\#SBATCH --mem=50gb
-\#SBATCH --output=BwaMem.%J.out
-\#SBATCH --error=BwaMem.%J.err
-
-
-
-| |
-|---------------------|
-| module load bwa/0.7 |
-
-bwa mem index\_prefix input\_reads\_pair\_1.fastq
-input\_reads\_pair\_2.fastq -t $SLURM\_NTASKS\_PER\_NODE >
-bwa\_mem\_alignments.sam
-
-
-
-****BWA Bwasw:****
-
-The **bwa bwasw** algorithm is another algorithm provided by BWA. For
-input files with single-end reads it aligns the query sequences. For
-input files with paired-ends reads it performs paired-end alignment that
-only works for Illumina reads. An example of **bwa bwasw** for
-single-end input file **input-reads.fasta** in fasta format and output
-file **bwa\_bwasw\_alignments.sam** where the alignments are stored, is
-shown below:
-
-**General BWA Bwasw Usage**
-
-``` syntaxhighlighter-pre
-bwa bwasw index_prefix input_reads.fasta -t $SLURM_NTASKS_PER_NODE > bwa_bwasw_alignments.sam
-```
-
-**
-**
-
-**BWA Aln:**
-
-The third BWA algorithm, **bwa aln**, aligns the input file of sequence
-data to the reference genome. In addition, there is an example of
-running **bwa aln** with single-end **input\_reads.fasta** input file
-and 8 CPUs:
-
-**General BWA Aln Usage**
-
-``` syntaxhighlighter-pre
-bwa aln index_prefix input_reads.fasta -0 -t $SLURM_NTASKS_PER_NODE > bwa_aln_alignments.sai
-```
-
-The command **bwa samse** uses the **bwa\_aln\_alignments.sai** output
-form **bwa aln** in order to generate SAM file from the alignments for
-single-end reads.
-
-**General BWA Samse Usage**
-
-``` syntaxhighlighter-pre
-bwa samse -f bwa_aln_alignments.sam index_prefix bwa_aln_alignments.sai input_reads.fasta
-```
-
-The command **bwa sampe** uses the **bwa\_aln\_alignments.sai** output
-form **bwa aln** in order to generate SAM file from the alignments for
-paired-end reads.
-
-**General BWA Sampe Usage**
-
-``` syntaxhighlighter-pre
-bwa samse -f bwa_aln_alignments.sam index_prefix bwa_aln_alignments_pair_1.sai bwa_aln_alignments_pair_2.sai input_reads_pair_1.fasta input_reads_pair_2.fasta
-```
-
-****
-****
-
-**BWA Fastmap:**
-
-The command **bwa fastmap** identifies and outputs super-maximal exact
-matches (SMEMs).
-
-**General BWA Fastmap Usage**
-
-``` syntaxhighlighter-pre
-bwa fastmap index_prefix input_reads.fasta > bwa_fastmap.matches
-```
-
-**
-**
-
-**BWA Pemerge:**
-
-The command **bwa pemerge** merges overlapping paired ends and can print
-either only the merged reads or the unmerged ones. An example of **bwa
-pemerge** of **input\_reads\_pair\_1.fastq**
-and **input\_reads\_pair\_2.fastq** with 8 CPUs and output
-file **output\_reads\_merged.fastq** that contains only the merged reads
-is shown below:
-
-**General BWA Pemerge Usage**
-
-``` syntaxhighlighter-pre
-bwa pemerge -m input_reads_pair_1.fastq input_reads_pair_2.fastq -t $SLURM_NTASKS_PER_NODE > output_reads_merged.fastq
-```
-
-
-
-**BWA Fa2pac:**
-
-The command **bwa fa2pac** converts fasta to pac files.
-
-**General BWA Pac2pac Usage**
-
-``` syntaxhighlighter-pre
-bwa fa2pac input_reads.fasta pac_prefix
-```
-
-
-
-**BWA Pac2bwt and **BWA Pac2bwtgen**:**
-
-The commands **bwa pac2bwt** and **bwa pac2bwtgen** convert pac to bwt
-files.
-
-**General BWA Pac2bwt Usage**
-
-``` syntaxhighlighter-pre
-bwa pac2bwt input_reads.pac output_reads.bwt
-```
-
-**General BWA Pac2bwtgen Usage**
-
-``` syntaxhighlighter-pre
-bwa pac2bwtgen input_reads.pac output_reads.bwt
-```
-
-
-
-**BWA Bwtupdate:**
-
-The command **bwa bwtupdate** updates bwt files to the new format.
-
-**General BWA Bwtupdate Usage**
-
-``` syntaxhighlighter-pre
-bwa bwtupdate input_reads.bwt
-```
-
-**
-**
-
-**BWA Bwt2sa:**
-
-The command **bwa bwt2sa** generates sa files from bwt and Occ files.
-
-**General BWA Bwt2sa Usage**
-
-``` syntaxhighlighter-pre
-bwa bwt2sa input_reads.bwt output_reads.sa
-```
-
-
-
-**Useful Information**
-
-In order to test the scalability of BWA (bwa/0.7) on Crane, we used two
-paired-end input fastq files: **large\_1.fastq** and **large\_2.fastq**,
-and one single-end input fasta file, **large.fasta**. Some statistics
-about the input files and the time and memory resources required
-for *bwa mem* are shown on the table below:
-
-
-
-**total \# of sequences**
-
-**total size in MB**
-
-<span style="color: rgb(0,0,0);">\# of used CPUs</span>
-
-running time for 4 CPUs
-
-required memory for 4 CPUs
-
-<span style="color: rgb(0,0,0);">\# of used CPUs</span>
-
-running time for 8 CPUs
-
-required memory for 8 CPUs
-
-<span style="color: rgb(0,0,0);">\# of used CPUs</span>
-
-running time for 16 CPUs
-
-required memory for 16 CPUs
-
-**large\_1.fastq**
-
-10,174,715
-
-3,376 MB
-
-4
-
-\~ 35 minutes
-
-\~ 12 GB
-
-8
-
-\~ 18.5 minutes
-
-\~ 18 GB
-
-16
-
-\~ 10 minutes
-
-\~ 19 GB
-
-**large\_2.fastq**
-
-10,174,715
-
-3,376 MB
-
-**large.fasta**
-
-592,593
-
-836 MB
-
-4
-
-\~ 5.5 minutes
-
-\~ 3 GB
-
-8
-
-\~ 3 minutes
-
-\~ 4 GB
-
-16
-
-\~ 2 minutes
-
-\~ 6.2 GB
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_bwa\_module.xsl](attachments/8193296/8127565.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193296/8127566.xml)
-(application/octet-stream)
+The command **bwa bwt2sa** generates sa files from bwt and Occ files. The basic usage of **bwa bwt2sa** is:
+{{< highlight bash >}}
+$ bwa bwt2sa input_reads.bwt output_reads.sa
+{{< /highlight >}}
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Useful Information</span>
+In order to test the scalability of BWA (bwa/0.7) on Crane, we used two paired-end input fastq files, `large_1.fastq` and `large_2.fastq`, and one single-end input fasta file, `large.fasta`. Some statistics about the input files and the time and memory resources used by **bwa mem** are shown on the table below:
+{{< readfile file="/static/html/bwa.html" >}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/clustal_omega.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/clustal_omega.md
index 754383c536e08f64db9cb7602d53bd3022288a00..717c7eb8858bb1a6f6a9e97fdada706cc600828f 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/clustal_omega.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/clustal_omega.md
@@ -1,199 +1,66 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Alignment Tools](Alignment-Tools_8193288.html)
++++
+title = "Clustal Omega"
+description = "How to run Clustal Omega on HCC resources"
+weight = "10"
++++
-<span id="title-text"> HCC-DOCS : Clustal Omega </span>
-=======================================================
-
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
-
-| Name | Version | Resource |
-|---------------|---------|----------|
-| clustal-omega | 1.2 | Tusker |
-
-| | | |
-|---------------|-----|-------|
-| clustal-omega | 1.2 | Crane |
-
-
-
-Clustal Omega
-(<a href="http://www.clustal.org/omega/" class="external-link">http://www.clustal.org/omega/</a>)
-is a general purpose multiple sequence alignment (MSA) tool used mainly
-with protein, as well as DNA and RNA sequences. Clustal Omega is fast
-and scalable aligner that can align datasets of hundreds of thousands of
-sequences in reasonable time.
+[Clustal Omega] (http://www.clustal.org/omega/) is a general purpose multiple sequence alignment (MSA) tool used mainly with protein, as well as DNA and RNA sequences. Clustal Omega is fast and scalable aligner that can align datasets of hundreds of thousands of sequences in reasonable time.
The general usage of Clustal Omega is:
+{{< highlight bash >}}
+$ clustalo -i input_file.fasta -o output_file.fasta [options]
+{{< /highlight >}}
+where **input_file.fasta** is the multiple sequence input file in `fasta` format, and **output_file.fasta** is the multiple sequence alignment output file in `fasta` format.
-**General Clustal Omega Usage**
-
-``` syntaxhighlighter-pre
-clustalo -i input_file.fasta -o output_file.fasta [options]
-```
-
-where **input\_file.fasta** is the multiple sequence input file in
-*fasta* format, and **output\_file.fasta** is the multiple sequence
-alignment output file in *fasta* format.
+\\
Clustal Omega accepts 3 types of sequence input files:
-- sequence file with aligned/unaligned sequences
-
-<!-- -->
+- sequence file with aligned/unaligned sequences
+- multiple alignment in a file/profile of aligned sequences
+- Hidden Markov Model (HMM)
-- multiple alignment in a file/profile of aligned sequences
-
-<!-- -->
-
-- Hidden Markov Model (HMM)
-
-These input files must contain at least 2 sequences and must be in one
-of the following MSA file formats: **a2m**, **fa\[sta\]**,
-**clu\[stal\]**, **msf**, **phy\[lip\]**, **selex**, **st\[ockholm\]**,
-**vie\[nna\]**. Moreover, if not specified, the generated output file is
-in *fasta* format.
+These input files must contain at least 2 sequences and must be in one of the following MSA file formats: `a2m`, `fa[sta]`, `clu[stal]`, `msf`, `phy[lip]`, `selex`, `st[ockholm]`, `vie[nna]`. Moreover, if not specified, the generated output file is in `fasta` format.
+\\
More Clustal Omega options can be found by typing:
-
-**Additional Clustal Omega Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.tusker~]$ clustalo -h
-```
-
-
-Running Clustal Omega on Tusker with input
-file **input\_reads.fasta** with **8 threads** and **10GB memory** is
-shown below:
-
-**clustal\_omega.submit**
-
-\#!/bin/sh
-\#SBATCH --job-name=Clustal\_Omega
-\#SBATCH --nodes=1
-\#SBATCH --ntasks-per-node=8
-\#SBATCH --time=10:00:00
-\#SBATCH --mem=10gb
-\#SBATCH --output=ClustalOmega.%J.out
-\#SBATCH --error=ClustalOmega.%J.err
-
-
-
-| |
-|-------------------------------|
-| module load clustal-omega/1.2 |
-
-clustalo -i input\_reads.fasta -o output\_msa.sto --outfmt=st
---threads=$SLURM\_NTASKS\_PER\_NODE
-
-The output file **output\_msa.sto** contains the resulting multiple
-sequence alignments in Stockholm format (**--outfmt=st**).
+{{< highlight bash >}}
+$ clustalo -h
+{{< /highlight >}}
+
+\\
+Running Clustal Omega on Tusker with input file `input_reads.fasta` with `8 threads` and `10GB memory` is shown below:
+{{% panel header="`clustal_omega.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=Clustal_Omega
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+#SBATCH --time=10:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=ClustalOmega.%J.out
+#SBATCH --error=ClustalOmega.%J.err
+
+module load clustal-omega/1.2
+
+clustalo -i input_reads.fasta -o output_msa.sto --outfmt=st --threads=$SLURM_NTASKS_PER_NODE
+{{< /highlight >}}
+{{% /panel %}}
+
+The output file `output_msa.sto` contains the resulting multiple sequence alignments in Stockholm format (**--outfmt=st**).
Moreover, if you change the command above with:
+{{< highlight bash >}}
+$ clustalo -i input_reads.sto --dealign -v
+{{< /highlight >}}
+Clustal Omega will read the input file in Stockholm format, de-align the sequences, and then re-align them, printing progress report in meanwhile (**-v**). Because it is not specified, the output will be in the default `fasta` format.
-**Clustal Omega with De-align Option**
-
-``` syntaxhighlighter-pre
-clustalo -i input_reads.sto --dealign -v
-```
-
-Clustal Omega will read the input file in Stockholm format, de-align the
-sequences, and then re-align them, printing progress report in meanwhile
-(**-v**). Because it is not specified, the output will be in the default
-**fasta** format.
-
-
-
-**Clustal Omega Output**
-
-The basic Clustal Omega output produces one alignment file in the
-specified output format. More intermediate outputs can be generated
-using specific Clustal Omega options, such
-as: **--distmat-out=<file>** (*pairwise distance matrix output
-file*) and **--guidetree-out=<file>** (*guide tree output file*).
-
-**
-Useful Information**
-
-In order to test the Clustal Omega performance on Tusker, we used three
-DNA and protein input fasta files: **data\_1. fasta, data\_2. fasta,
-data\_3.fasta**. Some statistics about the input files and the time and
-memory resources required for Clustal Omega are shown on the table
-below:
-
-<table style="width:100%;">
-<colgroup>
-<col style="width: 14%" />
-<col style="width: 14%" />
-<col style="width: 14%" />
-<col style="width: 14%" />
-<col style="width: 14%" />
-<col style="width: 14%" />
-<col style="width: 14%" />
-</colgroup>
-<thead>
-<tr class="header">
-<th> </th>
-<th><p><strong>total # of sequences</strong></p></th>
-<th><p><strong>average sequence length</strong></p></th>
-<th><p><strong>total size in MB</strong></p></th>
-<th><p><strong>Clustal Omega required time</strong></p></th>
-<th><p><strong>Clustal Omega required memory</strong></p></th>
-<th># of used CPUs</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><p><strong>data_1.fasta</strong></p></td>
-<td><p>1,200</p></td>
-<td><p>510.17</p></td>
-<td><p>641 KB</p></td>
-<td><p>~ 5 minutes</p></td>
-<td><span>~ 65 MB</span></td>
-<td>8</td>
-</tr>
-<tr class="even">
-<td><p><strong>data_2.fasta</strong></p></td>
-<td><p>5,715</p></td>
-<td><p>174.20</p></td>
-<td><p>1,100 KB</p></td>
-<td>~ 5 minutes</td>
-<td><p>~ 140 MB</p></td>
-<td><p>8</p></td>
-</tr>
-<tr class="odd">
-<td><p><strong>data_3.fasta</strong></p></td>
-<td><p>93,675</p></td>
-<td><p>94.29</p></td>
-<td><p>11,000 KB</p></td>
-<td><p>~ 30 minutes</p></td>
-<td><p>~ 2 GB</p></td>
-<td><p>8</p></td>
-</tr>
-</tbody>
-</table>
-
-Attachments:
-------------
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Clustal Omega Output</span>
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_clustal\_omega\_version.xsl](attachments/9470379/9863812.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_clustal\_omega\_module.xsl](attachments/9470379/9863813.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_clustal\_omega\_version.xsl](attachments/9470379/9863814.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/9470379/9863815.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/9470379/9863816.xml)
-(application/octet-stream)
+The basic Clustal Omega output produces one alignment file in the specified output format. More intermediate outputs can be generated using specific Clustal Omega options, such as: **--distmat-out=<file>** (*pairwise distance matrix output file*) and **--guidetree-out=<file>** (*guide tree output file*).
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Useful Information</span>
+In order to test the Clustal Omega performance on Tusker, we used three DNA and protein input fasta files, `data_1.fasta`, `data_2.fasta`, `data_3.fasta`. Some statistics about the input files and the time and memory resources used by Clustal Omega on Tusker are shown on the table below:
+{{< readfile file="/static/html/clustal_omega.html" >}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
index 00773e5a4c36769b3dc1b4f35196af57f42dfcd2..294371c7e9c64cb9405d2798768f860851878a06 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
@@ -1,1015 +1,59 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Alignment Tools](Alignment-Tools_8193288.html)
++++
+title = "TopHat/TopHat2"
+description = "How to run TopHat/TopHat2 on HCC resources"
+weight = "10"
++++
-<span id="title-text"> HCC-DOCS : TopHat/TopHat2 </span>
-========================================================
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
+[TopHat] (https://ccb.jhu.edu/software/tophat/index.shtml) is a fast splice junction mapper for RNA-Seq data. It first aligns RNA-Seq reads to reference genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
-| Name | Version | Resource |
-|--------|---------|----------|
-| tophat | 2.0.14 | Tusker |
-| tophat | 2.1.1 | Tusker |
+Although there is no difference between the available options for both TopHat and TopHat2 and the number of output files, TopHat2 incorporates many significant improvements to TopHat. The TopHat package at HCC supports both **tophat** and **tophat2**.
-| | | |
-|--------|-------|-------|
-| tophat | 2.0 | Crane |
-| tophat | 2.1.0 | Crane |
+The basic usage of TopHat2 is:
+{{< highlight bash >}}
+$ [tophat|tophat2] [options] index_prefix [input_reads_pair_1.[fasta|fastq] input_reads_pair_2.[fasta|fastq] | input_reads.[fasta|fastq]]
+{{< /highlight >}}
+where **index_prefix** is the basename of the genome index to be searched. This index is generated prior running TopHat/TopHat2 by using [Bowtie](bowtie)/[Bowtie2](bowtie2).
-
+TopHat2 uses single or comma-separated list of paired-end and single-end reads in fasta or fastq format. The single-end reads need to be provided after the paired-end reads.
-TopHat
-(<a href="http://ccb.jhu.edu/software/tophat/index.shtml" class="external-link">http://ccb.jhu.edu/software/tophat/index.shtml</a>)
-is a fast splice junction mapper for RNA-Seq data. It first aligns
-RNA-Seq reads to reference genomes using the ultra high-throughput short
-read aligner Bowtie, and then analyzes the mapping results to identify
-splice junctions between exons. Although there is no difference between
-the available options for both TopHat and TopHat2 and the number of
-output files, TopHat2 incorporates many significant improvements to
-TopHat. The TopHat package at HCC supports both **tophat** and
-**tophat2**.
+More advanced TopHat2 options can be found in [its manual] (https://ccb.jhu.edu/software/tophat/manual.shtml), or by typing:
+{{< highlight bash >}}
+$ tophat2 -h
+{{< /highlight >}}
-The basic usage of TopHat2 is:
+Prior running TopHat/TopHat2, an index from the reference genome should be built using Bowtie/Bowtie2. Moreover, TopHat2 requires both, the index file and the reference file, to be in the same directory. If the reference file is not available,TopHat2 reconstructs it in its initial step using the index file.
-**General TopHat2 Usage**
+\\
+An example of how to run TopHat2 on Tusker with paired-end fastq files `input_reads_pair_1.fastq` and `input_reads_pair_2.fastq`, reference index `index_prefix` and `8 CPUs` is shown below:
+{{% panel header="`tophat2_alignment.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=Tophat2
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=Tophat2.%J.out
+#SBATCH --error=Tophat2.%J.err
-``` syntaxhighlighter-pre
-[tophat|tophat2] [options] index_prefix [input_reads_pair_1.[fasta|fastq] input_reads_pair_2.[fasta|fastq] | input_reads.[fasta|fastq]]
-```
+module load samtools/1.3 bowtie/2.3 tophat/2.0
-where **index\_prefix** is the basename of the genome index to be
-searched. This index is generated prior running TopHat/TopHat2 by using
-[Bowtie](Bowtie_8193293.html)/[Bowtie2](Bowtie2_8193294.html). TopHat2
-uses single or comma-separated list of paired-end and single-end reads
-in fasta or fastq format. The single-end reads need to be provided after
-the paired-end reads. More advanced TopHat2 options can be found in the
-manual: <a href="http://ccb.jhu.edu/software/tophat/manual.shtml" class="external-link">http://ccb.jhu.edu/software/tophat/manual.shtml</a>,
-or by typing:
+tophat2 -p $SLURM_NTASKS_PER_NODE index_prefix input_reads_pair_1.fastq input_reads_pair_2.fastq
+{{< /highlight >}}
+{{% /panel %}}
-**Additional TopHat2 Options**
+TopHat2 generates its own output directory `tophat_output/` that contains multiple TopHat2 generated files.
-``` syntaxhighlighter-pre
-[<username>@login.tusker ~]$ tophat2 -h
-```
-
-Prior running TopHat/TopHat2, an index from the reference genome should
-be built using Bowtie/Bowtie2. Moreover, TopHat2 requires both, the
-index file and the reference file, to be in the same directory. If the
-reference file is not available,TopHat2 reconstructs it in its initial
-step using the index file.
-
-An example of how to run TopHat2 on Tusker with paired-end fastq files
-**input\_reads\_pair\_1.fastq** and **input\_reads\_pair\_2.fastq**,
-reference index **index\_prefix** and 8 CPUs is shown below:
-
-**tophat2\_alignment.submit**
-
-\#!/bin/sh
-\#SBATCH --job-name=Tophat2
-\#SBATCH --nodes=1
-\#SBATCH --ntasks-per-node=8
-\#SBATCH --time=168:00:00
-\#SBATCH --mem=50gb
-\#SBATCH --output=Tophat2.%J.out
-\#SBATCH --error=Tophat2.%J.err
-
-
-
-| |
-|------------------------------------------------|
-| module load samtools/1.3 bowtie/2.3 tophat/2.0 |
-
-tophat2 -p $SLURM\_NTASKS\_PER\_NODE index\_prefix
-input\_reads\_pair\_1.fastq input\_reads\_pair\_2.fastq
-
-TopHat2 generates its own output directory *tophat\_output/* that
-contains multiple TopHat2 generated files.
-
-**
-**
-
-**TopHat2 Output**
-
-TopHat2 produces number of files in its *tophat\_out/* output directory.
-Some of the generated files are:
-
-- **accepted\_hits.bam**: list of read alignments in BAM format
-- **unmapped.bam**: list of unmapped reads in BAM format
-- **junctions.bed**: BED track of reported junctions**
- **
-- **insertions.bed**: BED track of insertions reported by TopHat
-- **deletions.bed**: BED track of deletions reported by TopHat
-- **prep\_reads.info**: statistis about the input sequencing data
- (min/max read length, number of reads)
-- **align\_summary.txt**: summary of the alignment counts (number of
- mapped reads, overall read mapping rate)
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/8127568.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/8127570.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_tophat2\_version.xsl](attachments/8193297/8127571.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_tophat2\_module.xsl](attachments/8193297/9863623.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/17044387.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193297/17044423.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/17044491.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/17044527.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/17044587.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/17044623.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/17044684.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/17044720.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/17044784.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/17044820.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193297/17044937.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193297/17044973.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/17047006.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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-[tusker\_modules.xml](attachments/8193297/18546712.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193297/18546855.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193297/18546917.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18547020.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18546988.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18547224.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18547093.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18547162.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18547347.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18547276.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18547413.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18547493.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18547458.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18547559.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18547594.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18547659.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18547694.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18547769.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18547804.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18547930.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18547865.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18547965.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18548030.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18548129.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18548094.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18548213.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18548248.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18548313.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18548349.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18548459.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18548494.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18548659.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18548581.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18548694.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18548759.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/18548794.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18548919.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193297/18548854.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193297/18548995.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18548960.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/18549079.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193297/20709466.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193297/20709428.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193297/20709532.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193297/20709568.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193297/21069844.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193297/21069883.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193297/21069962.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193297/21070001.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193297/21070100.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193297/21070139.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193297/21070212.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193297/21070251.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193297/21070341.xml) (text/xml)
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-[crane\_modules.xml](attachments/8193297/21070409.xml) (text/xml)
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-[tusker\_modules.xml](attachments/8193297/33686077.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/33686150.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/33686181.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/33686289.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/33686320.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/33687825.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/33687856.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/33688432.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/33688465.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/33689758.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/33689789.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/33689978.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/33690009.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35323987.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/35324049.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35324097.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/35324159.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35324435.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/35324629.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35324565.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35324855.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/35324919.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35325020.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/35325651.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35325189.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35325232.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35325275.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35325582.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35325454.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/35325671.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35325606.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35325480.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35325499.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35325532.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35325869.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35325699.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35325723.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/35325764.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/35325784.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35326160.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35326184.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/35326751.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/35326771.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35325888.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35325916.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35325935.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35325966.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326024.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326095.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326208.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35326686.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35326710.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326310.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326404.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326432.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326500.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326550.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326589.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326640.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326662.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326820.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/17044372.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193297/35325373.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/17044373.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193297/35325372.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326897.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326932.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35326951.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35327033.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193297/35325369.xml) (text/xml)
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">TopHat2 Output</span>
+TopHat2 produces number of files in its `tophat_out/` output directory. Some of the generated files are:
+- **accepted_hits.bam**: list of read alignments in BAM format
+- **unmapped.bam**: list of unmapped reads in BAM format
+- **junctions.bed**: BED track of reported junctions
+- **insertions.bed**: BED track of insertions reported by TopHat
+- **deletions.bed**: BED track of deletions reported by TopHat
+- **prep_reads.info**: statistics about the input sequencing data (min/max read length, number of reads)
+- **align_summary.txt**: summary of the alignment counts (number of mapped reads, overall read mapping rate)
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/_index.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/_index.md
index b91b407b74b24fd6f807d0547b2d3e8fcbe10c0d..720054069b4f54c10df594a5d508beab288e82df 100644
--- a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/_index.md
@@ -1,18 +1,7 @@
+++
title = "Data Manipulation Tools"
+description = "How to use data manipulation tools on HCC machines"
+weight = "52"
+++
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-
-<span id="title-text"> HCC-DOCS : Data Manipulation Tools </span>
-=================================================================
-
-Created by <span class="author"> Adam Caprez</span> on Sep 04, 2014
-
-
-
-
+{{% children %}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
index e781ae15bc96c3f51af9124f018d6f3fc6bf93ca..c1e0d2142bc421f791dd0831f750166e01f51788 100644
--- a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
@@ -1,147 +1,36 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Data Manipulation Tools](Data-Manipulation-Tools_8193304.html)
-
-<span id="title-text"> HCC-DOCS : BamTools </span>
-==================================================
-
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
-
-| Name | Version | Resource |
-|----------|---------|----------|
-| bamtools | 2.3.0 | Tusker |
-| bamtools | 2.4.1 | Tusker |
-
-| | | |
-|----------|-------|-------|
-| bamtools | 2.3.0 | Crane |
-| bamtools | 2.4.1 | Crane |
-
++++
+title = "BamTools"
+description = "How to use BamTools on HCC machines"
+weight = "52"
++++
-The SAM/BAM format is a standard format for short read alignments. While
-SAM is the plain-text version of the alignments, BAM is compressed,
-binary format of the alignments that is used for space-saving. BamTools
-is a toolkit for handling BAM files. BamTools provides a powerful suite
-of command-lines programs for manipulating and querying BAM files for
-data.
+The SAM/BAM format is a standard format for short read alignments. While SAM is the plain-text version of the alignments, BAM is compressed, binary format of the alignments that is used for space-saving. BamTools is a toolkit for handling BAM files. BamTools provides a powerful suite of command-lines programs for manipulating and querying BAM files for data.
The basic usage of BamTools is:
-
-**General BamTools Usage**
-
-``` syntaxhighlighter-pre
-bamtools COMMAND [options]
-```
-
-where **COMMAND** is one of the following BamTools commands**:**
-
-- **convert**: Converts between BAM and a number of other formats
-- **count**: Prints number of alignments in BAM file(s)
-- **coverage**: Prints coverage statistics from the input BAM file
-- **filter**: Filters BAM file(s) by user-specified criteria
-- **header**: Prints BAM header information
-- **index**: Generates index for BAM file
-- **merge**: Merge multiple BAM files into single file
-- **random**: Select random alignments from existing BAM file(s),
- intended more as a testing tool
-- **resolve**: Resolves paired-end reads (marking the IsProperPair
- flag as needed)
-- **revert**: Removes duplicate marks and restores original base
- qualities
-- **sort**: Sorts the BAM file according to some criteria
-- **split**: Splits a BAM file on user-specified property, creating a
- new BAM output file for each value found
-- **stats**: Prints some basic statistics from input BAM file(s)
-
-For detailed description and more information on a specific command,
-just type:
-
-**General BamTools COMMAND Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.tusker~]$ bamtools help COMMAND
-```
-
-or check the BamTools web
-site: <a href="https://github.com/pezmaster31/bamtools/wiki" class="external-link">https://github.com/pezmaster31/bamtools/wiki</a>.
-
-The page [Running BamTools
-Commands](Running-BamTools-Commands_8193306.html) shows how to run
-BamTools on HCC.
-
-
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_bamtools\_version.xsl](attachments/8193305/8127591.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193305/8127592.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_bamtools\_version.xsl](attachments/8193305/8127593.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193305/8127594.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35325459.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35325485.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35325504.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35325537.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35325874.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35325893.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35325921.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35325940.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35325971.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326029.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326100.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326213.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326315.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326409.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326437.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326505.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326555.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326594.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326645.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326667.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326825.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326902.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326937.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35326956.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35327038.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193305/35325385.xml) (text/xml)
-
-
+{{< highlight bash >}}
+$ bamtools COMMAND [options]
+{{< /highlight >}}
+where **COMMAND** is one of the following BamTools commands:
+
+- **convert**: Converts between BAM and a number of other formats
+- **count**: Prints number of alignments in BAM file(s)
+- **coverage**: Prints coverage statistics from the input BAM file
+- **filter**: Filters BAM file(s) by user-specified criteria
+- **header**: Prints BAM header information
+- **index**: Generates index for BAM file
+- **merge**: Merge multiple BAM files into single file
+- **random**: Select random alignments from existing BAM file(s), intended more as a testing tool
+- **resolve**: Resolves paired-end reads (marking the IsProperPair flag as needed)
+- **revert**: Removes duplicate marks and restores original base qualities
+- **sort**: Sorts the BAM file according to some criteria
+- **split**: Splits a BAM file on user-specified property, creating a new BAM output file for each value found
+- **stats**: Prints some basic statistics from input BAM file(s)
+
+For detailed description and more information on a specific command, just type:
+{{< highlight bash >}}
+$ bamtools help COMMAND
+{{< /highlight >}}
+or check the BamTools web, https://github.com/pezmaster31/bamtools/wiki.
+
+The page [Running BamTools Commands](running_bamtools_commands) shows how to run BamTools on HCC.
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md
index dbf753706737f54aab4669a94522a7b68fc3e64e..249019029d2cb066e7588cc04b1d529cd08b8489 100644
--- a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/running_bamtools_commands.md
@@ -1,285 +1,143 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Data Manipulation Tools](Data-Manipulation-Tools_8193304.html)
-7. [BamTools](BamTools_8193305.html)
++++
+title = "Running BamTools Commands"
+description = "How to run BamTools commands on HCC resources"
+weight = "10"
++++
-<span id="title-text"> HCC-DOCS : Running BamTools Commands </span>
-===================================================================
-
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
-
-**BamTools Convert:**
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BamTools Convert:</span>
One of the most frequently used BamTools command is **convert**.
The basic usage of the BamTools **convert** is:
-
-**General BamTools Convert Usage**
-
-``` syntaxhighlighter-pre
-bamtools convert -format [bed|fasta|fastq|json|pileup|sam|yaml] -in input_alignments.bam -out output_reads.[bed|fasta|fastq|json|pileup|sam|yaml]
-```
-
-where the option **-format** specifies the type of the output
-file, **input\_alignments.bam** is the input BAM file,
-and **-out** defines the name and the type of the converted file.
-
-Running BamTools **convert** on Tusker with input
-file **input\_alignments.bam** and output
-file **output\_reads.fastq** is shown below:
-
-**bamtools\_convert.submit**
-
-\#!/bin/sh
-\#SBATCH --job-name=BamTools\_Convert
-\#SBATCH --nodes=1
-\#SBATCH --ntasks-per-node=1
-\#SBATCH --time=168:00:00
-\#SBATCH --mem=20gb
-\#SBATCH --output=BamTools.%J.out
-\#SBATCH --error=BamTools.%J.err
-
-
-
-| |
-|--------------------------|
-| module load bamtools/2.4 |
-
-bamtools convert -format fastq -in input\_alignments.bam -out
-output\_reads.fastq
-
-All BamTools commands are single threaded, and therefore both **\#SBATCH
---nodes** and **\#SBATCH --ntasks-per-node** are set to **1**.
-
-
-
-**BamTools Count:**
-
-**BamTools Count Command**
-
-``` syntaxhighlighter-pre
-bamtools count -in input_alignments.bam
-```
-
-The command **bamtools count** outputs the total number of alignments in
-the BAM file.
-
-
-
-**BamTools Coverage:**
-
-**BamTools Coverage Command**
-
-``` syntaxhighlighter-pre
-bamtools coverage -in input_alignments.bam -out output_reads_coverage.txt
-```
-
-The command **bamtools coverage **prints the coverage data for a single
-BAM file
-
-
-
-**BamTools Filter:**
-
-**BamTools Filter Command**
-
-``` syntaxhighlighter-pre
- bamtools filter -in input_alignments.bam -out output_alignments_filtered.bam -length 100
-```
-
-The command **bamtools filter** filters the BAM file based on specified
-options. In this example, the resulting bam
-file **output\_alignments\_filtered.bam** contains alignments with
-length more than 100.
-
-
-
-**BamTools Header:**
-
-**BamTools Header Command**
-
-``` syntaxhighlighter-pre
- bamtools header -in input_alignments.bam -out output_alignments_header.txt
-```
-
+{{< highlight bash >}}
+$ bamtools convert -format [bed|fasta|fastq|json|pileup|sam|yaml] -in input_alignments.bam -out output_reads.[bed|fasta|fastq|json|pileup|sam|yaml]
+{{< /highlight >}}
+where the option **-format** specifies the type of the output file, **input_alignments.bam** is the input BAM file, and **-out** defines the name and the type of the converted file.
+
+Running BamTools **convert** on Tusker with input file `input_alignments.bam` and output file `output_reads.fastq` is shown below:
+{{% panel header="`bamtools_convert.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=BamTools_Convert
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=BamTools.%J.out
+#SBATCH --error=BamTools.%J.err
+
+module load bamtools/2.4
+
+bamtools convert -format fastq -in input_alignments.bam -out output_reads.fastq
+{{< /highlight >}}
+{{% /panel %}}
+
+All BamTools commands are single threaded, and therefore both `#SBATCH --nodes` and `#SBATCH --ntasks-per-node` are set to **1**.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BamTools Count:</span>
+
+The basic usage of the BamTools **count** is:
+{{< highlight bash >}}
+$ bamtools count -in input_alignments.bam
+{{< /highlight >}}
+The command **bamtools count** outputs the total number of alignments in the BAM file.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BamTools Coverage:</span>
+
+The basic usage of the BamTools **coverage** is:
+{{< highlight bash >}}
+$ bamtools coverage -in input_alignments.bam -out output_reads_coverage.txt
+{{< /highlight >}}
+The command **bamtools coverage **prints the coverage data for a single BAM file.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BamTools Filter:</span>
+
+The basic usage of the BamTools **filter** is:
+{{< highlight bash >}}
+$ bamtools filter -in input_alignments.bam -out output_alignments_filtered.bam -length 100
+{{< /highlight >}}
+The command **bamtools filter** filters the BAM file based on specified options. In this example, the resulting bam file `output_alignments_filtered.bam` contains alignments with length longer than 100 base pairs.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BamTools Header:</span>
+
+The basic usage of the BamTools **header** is:
+{{< highlight bash >}}
+$ bamtools header -in input_alignments.bam -out output_alignments_header.txt
+{{< /highlight >}}
The command **bamtools header** prints the header from BAM file.
-
-
-**BamTools Index:**
-
-**BamTools Index Command**
-
-``` syntaxhighlighter-pre
- bamtools index -in input_alignments.bam
-```
-
-The command **bamtools index** creates index for BAM file and prints
-**input\_alignments.bam.bai** file.
-
-
-
-**BamTools Merge:**
-
-**BamTools Merge Command**
-
-``` syntaxhighlighter-pre
- bamtools merge -in input_alignments_1.bam -in input_alignments_2.bam -in input_alignments_3.bam -out output_alignments_merged.bam
-```
-
-The command **bamtools merge** merges multiple (more than 2) BAM files
-into one.
-
-
-
-**BamTools Random:**
-
-**BamTools Random Command**
-
-``` syntaxhighlighter-pre
- bamtools random -in input_alignments.bam -out output_alignments_100.bam -n 100
-```
-
-The command **bamtools random** grabs a random subset of alignments.
-With the option **-n 100**, 100 randomly chosen alignments are stored in
-the output file **output\_alignments\_100.bam**.
-
-
-
-**BamTools Resolve:**
-
-**BamTools Resolve Command**
-
-``` syntaxhighlighter-pre
- bamtools resolve -twoPass -in input_alignments.bam -out output_alignments.bam
-```
-
-The command **bamtools resolve** resolves paired-end reads. The
-resolving mode is required, and it can be **-makeStats**,
-**-markPairs**, or **-twoPass**.
-
-**
-**
-
-**BamTools Revert:**
-
-**BamTools Revert Command**
-
-``` syntaxhighlighter-pre
- bamtools revert -in input_alignments.bam -out output_alignments_reverted.bam
-```
-
-The command **bamtools revert** removes duplicate marks and restores
-original base qualities.
-
-
-
-**BamTools Sort:**
-
-**BamTools Sort Command**
-
-``` syntaxhighlighter-pre
- bamtools sort -in input_alignments.bam -out output_alignments_sorted.bam -byname
-```
-
-The command **bamtools sort** sorts a BAM file according to a given
-option. **Output\_alignments\_sorted.bam** is the resulting file, where
-the alignments are sorted by name.
-
-
-
-**BamTools Split:**
-
-**BamTools Split Command**
-
-``` syntaxhighlighter-pre
- bamtools split -in input_alignments.bam -mapped
-```
-
-The command **bamtools split** splits BAM file on user-specified
-property and creates a new BAM output file for each value found. In the
-given example, an output file **input\_alignments.MAPPED.bam** is
-produced after -**mapped** split option is specified. Beside **mapped**,
-the split option can be: **-paired**, **-reference**, or **-tag
-<tag\_name>**.
-
-
-
-**BamTools Stats:**
-
-**BamTools Stats Command**
-
-``` syntaxhighlighter-pre
- bamtools stats -in input_alignments.bam
-```
-
-The command **bamtools stats** prints general alignment statistics from
-the BAM file.
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_bamtools\_module.xsl](attachments/8193306/8127595.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193306/8127596.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325460.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325486.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325505.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325538.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325875.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325894.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325922.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325941.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325972.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326030.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326101.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326214.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326316.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326410.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326438.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326506.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326556.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326595.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326646.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326668.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326826.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326903.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326938.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326957.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35327039.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325387.xml) (text/xml)
-
-
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BamTools Index:</span>
+
+The basic usage of the BamTools **index** is:
+{{< highlight bash >}}
+$ bamtools index -in input_alignments.bam
+{{< /highlight >}}
+The command **bamtools index** creates index for BAM file and prints `input_alignments.bam.bai` file.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BamTools Merge:</span>
+
+The basic usage of the BamTools **merge** is:
+{{< highlight bash >}}
+$ bamtools merge -in input_alignments_1.bam -in input_alignments_2.bam -in input_alignments_3.bam -out output_alignments_merged.bam
+{{< /highlight >}}
+The command **bamtools merge** merges multiple (more than 2) BAM files into one.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BamTools Random:</span>
+
+The basic usage of the BamTools **random** is:
+{{< highlight bash >}}
+$ bamtools random -in input_alignments.bam -out output_alignments_100.bam -n 100
+{{< /highlight >}}
+The command **bamtools random** grabs a random subset of alignments. With the option `-n 100`, 100 randomly chosen alignments are stored in the output file `output_alignments_100.bam`.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BamTools Resolve:</span>
+
+The basic usage of the BamTools **resolve** is:
+{{< highlight bash >}}
+$ bamtools resolve -twoPass -in input_alignments.bam -out output_alignments.bam
+{{< /highlight >}}
+The command **bamtools resolve** resolves paired-end reads. The resolving mode is required, and it can be `-makeStats`, `-markPairs`, or `-twoPass`.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BamTools Revert:</span>
+
+The basic usage of the BamTools **revert** is:
+{{< highlight bash >}}
+$ bamtools revert -in input_alignments.bam -out output_alignments_reverted.bam
+{{< /highlight >}}
+The command **bamtools revert** removes duplicate marks and restores original base qualities.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BamTools Sort:</span>
+
+The basic usage of the BamTools **sort** is:
+{{< highlight bash >}}
+$ bamtools sort -in input_alignments.bam -out output_alignments_sorted.bam -byname
+{{< /highlight >}}
+The command **bamtools sort** sorts a BAM file according to a given option. `output_alignments_sorted.bam` is the resulting file, where the alignments are sorted by name.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BamTools Split:</span>
+
+The basic usage of the BamTools **split** is:
+{{< highlight bash >}}
+$ bamtools split -in input_alignments.bam -mapped
+{{< /highlight >}}
+The command **bamtools split** splits BAM file on user-specified property and creates a new BAM output file for each value found. In the given example, an output file `input_alignments.MAPPED.bam` is produced after `-mapped` split option is specified. Beside `mapped`, the split option can be: `-paired`, `-reference`, or `-tag <tag_name>`.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">BamTools Stats:</span>
+
+The basic usage of the BamTools **stats** is:
+{{< highlight bash >}}
+$ bamtools stats -in input_alignments.bam
+{{< /highlight >}}
+The command **bamtools stats** prints general alignment statistics from the BAM file.
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
index 7c21414219bf564cf7c8570c428b001a60335b5b..a4fb2d1c459e7f2c0bf95e7e8ca5253f42771757 100644
--- a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
@@ -1,1096 +1,41 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Data Manipulation Tools](Data-Manipulation-Tools_8193304.html)
++++
+title = "SAMtools"
+description = "How to use SAMtools on HCC machines"
+weight = "52"
++++
-<span id="title-text"> HCC-DOCS : SAMtools </span>
-==================================================
-
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
-
-| Name | Version | Resource |
-|----------|---------|----------|
-| samtools | 0.1 | Tusker |
-| samtools | 1.1 | Tusker |
-| samtools | 1.2 | Tusker |
-| samtools | 1.3.1 | Tusker |
-
-| Name | Version | Resource |
-|----------|---------|----------|
-| samtools | 1.5 | Tusker |
-| samtools | 1.6 | Tusker |
-| samtools | 1.9 | Tusker |
-
-| | | |
-|----------|-------|-------|
-| samtools | 0.1 | Crane |
-| samtools | 1.1 | Crane |
-| samtools | 1.2 | Crane |
-| samtools | 1.3.1 | Crane |
-
-
-
-| | | |
-|----------|-----|-------|
-| samtools | 1.5 | Crane |
-| samtools | 1.6 | Crane |
-| samtools | 1.9 | Crane |
-
-The SAM format is a standard format for storing large nucleotide
-sequence alignments. The BAM format is just the binary form from SAM.
-SAMtools
-(<a href="http://samtools.sourceforge.net/" class="external-link">http://samtools.sourceforge.net/</a>)
-is a toolkit for manipulating alignments in SAM/BAM format, including
-sorting, merging, indexing and generating alignments in a per-position
-format.
+The SAM format is a standard format for storing large nucleotide sequence alignments. The BAM format is just the binary form from SAM. [SAMtools] (http://www.htslib.org/) is a toolkit for manipulating alignments in SAM/BAM format, including sorting, merging, indexing and generating alignments in a per-position format.
The basic usage of SAMtools is:
-
-**General SAMtools Usage**
-
-``` syntaxhighlighter-pre
-samtools COMMAND [options]
-```
-
+{{< highlight bash >}}
+$ samtools COMMAND [options]
+{{< /highlight >}}
where **COMMAND** is one of the following SAMtools commands**:**
-- **view**: SAM/BAM and BAM/SAM conversion
-- **sort**: sort alignment file
-- **mpileup**: multi-way pileup
-- **depth**: compute the depth
-- **faidx**: index/extract FASTA
-- **tview**: text alignment viewer
-- **index**: index alignment
-- **idxstats**: BAM index stats
-- **fixmate**: fix mate information
-- **flagstat**: simple stats
-- **calmd**: recalculate MD/NM tags and '=' bases
-- **merge**: merge sorted alignments
-- **rmdup**: remove PCR duplicates
-- **reheader**: replace BAM header
-- **cat**: concatenate BAMs
-- **bedcov**: read depth per BED region
-- **targetcut**: cut fosmid regions
-- **phase**: phase heterozygotes
-- **bamshuf**: shuffle and group alignments by name
-
-For detailed description and more information on a specific command,
-just type:
-
-**General SAMtools COMMAND Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.tusker~]$ samtools COMMAND
-```
-
-or check the SAMtools
-manual: <a href="http://samtools.sourceforge.net/samtools.shtml" class="external-link">http://samtools.sourceforge.net/samtools.shtml</a>.
-
-The page [Running SAMtools
-Commands](Running-SAMtools-Commands_8193308.html) shows how to run
-SAMtools on HCC.
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/8127597.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_samtools\_version.xsl](attachments/8193307/8127598.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/8127599.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_samtools\_version.xsl](attachments/8193307/8127600.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/17041705.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/17041737.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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-[crane\_modules.xml](attachments/8193307/33686035.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/33686067.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/33686139.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/33686171.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/33686278.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/33686310.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/33687814.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/33687846.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/33688420.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/33688454.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/33689747.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/33689779.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/33689967.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/33689999.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/35323976.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/35324039.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/35324086.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/35324149.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/35324424.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/35324619.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/35324554.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/35324844.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/35324909.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/35325009.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/35325641.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/35325178.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/35325221.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/35325264.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/35325571.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35325443.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35325469.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35325488.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35325521.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35325858.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/35325688.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/35325754.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/35326149.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/35326741.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35325877.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35325905.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35325924.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35325955.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326013.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326084.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326197.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/35326675.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326299.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326393.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326421.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326489.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326539.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326578.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326629.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326651.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326809.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193307/17041694.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193307/17041695.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326886.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326921.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35326940.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35327022.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193307/35325389.xml) (text/xml)
-
-
+- **view**: SAM/BAM and BAM/SAM conversion
+- **sort**: sort alignment file
+- **mpileup**: multi-way pileup
+- **depth**: compute the depth
+- **faidx**: index/extract FASTA
+- **tview**: text alignment viewer
+- **index**: index alignment
+- **idxstats**: BAM index stats
+- **fixmate**: fix mate information
+- **flagstat**: simple stats
+- **calmd**: recalculate MD/NM tags and '=' bases
+- **merge**: merge sorted alignments
+- **rmdup**: remove PCR duplicates
+- **reheader**: replace BAM header
+- **cat**: concatenate BAMs
+- **bedcov**: read depth per BED region
+- **targetcut**: cut fosmid regions
+- **phase**: phase heterozygotes
+- **bamshuf**: shuffle and group alignments by name
+
+For detailed description and more information on a specific command, just type:
+{{< highlight bash >}}
+$ samtools COMMAND
+{{< /highlight >}}
+or check the [SAMtools manual] (http://www.htslib.org/doc/samtools.html).
+
+The page [Running SAMtools Commands](running_samtools_commands) shows how to run SAMtools on HCC.
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/running_bamtools_commands.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/running_bamtools_commands.md
deleted file mode 100644
index dbf753706737f54aab4669a94522a7b68fc3e64e..0000000000000000000000000000000000000000
--- a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/running_bamtools_commands.md
+++ /dev/null
@@ -1,285 +0,0 @@
-1. [HCC-DOCS](index.html)
-2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
-3. [HCC Documentation](HCC-Documentation_332651.html)
-4. [Running Applications](Running-Applications_7471153.html)
-5. [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
-6. [Data Manipulation Tools](Data-Manipulation-Tools_8193304.html)
-7. [BamTools](BamTools_8193305.html)
-
-<span id="title-text"> HCC-DOCS : Running BamTools Commands </span>
-===================================================================
-
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Sep 07, 2018
-
-**BamTools Convert:**
-
-One of the most frequently used BamTools command is **convert**.
-
-The basic usage of the BamTools **convert** is:
-
-**General BamTools Convert Usage**
-
-``` syntaxhighlighter-pre
-bamtools convert -format [bed|fasta|fastq|json|pileup|sam|yaml] -in input_alignments.bam -out output_reads.[bed|fasta|fastq|json|pileup|sam|yaml]
-```
-
-where the option **-format** specifies the type of the output
-file, **input\_alignments.bam** is the input BAM file,
-and **-out** defines the name and the type of the converted file.
-
-Running BamTools **convert** on Tusker with input
-file **input\_alignments.bam** and output
-file **output\_reads.fastq** is shown below:
-
-**bamtools\_convert.submit**
-
-\#!/bin/sh
-\#SBATCH --job-name=BamTools\_Convert
-\#SBATCH --nodes=1
-\#SBATCH --ntasks-per-node=1
-\#SBATCH --time=168:00:00
-\#SBATCH --mem=20gb
-\#SBATCH --output=BamTools.%J.out
-\#SBATCH --error=BamTools.%J.err
-
-
-
-| |
-|--------------------------|
-| module load bamtools/2.4 |
-
-bamtools convert -format fastq -in input\_alignments.bam -out
-output\_reads.fastq
-
-All BamTools commands are single threaded, and therefore both **\#SBATCH
---nodes** and **\#SBATCH --ntasks-per-node** are set to **1**.
-
-
-
-**BamTools Count:**
-
-**BamTools Count Command**
-
-``` syntaxhighlighter-pre
-bamtools count -in input_alignments.bam
-```
-
-The command **bamtools count** outputs the total number of alignments in
-the BAM file.
-
-
-
-**BamTools Coverage:**
-
-**BamTools Coverage Command**
-
-``` syntaxhighlighter-pre
-bamtools coverage -in input_alignments.bam -out output_reads_coverage.txt
-```
-
-The command **bamtools coverage **prints the coverage data for a single
-BAM file
-
-
-
-**BamTools Filter:**
-
-**BamTools Filter Command**
-
-``` syntaxhighlighter-pre
- bamtools filter -in input_alignments.bam -out output_alignments_filtered.bam -length 100
-```
-
-The command **bamtools filter** filters the BAM file based on specified
-options. In this example, the resulting bam
-file **output\_alignments\_filtered.bam** contains alignments with
-length more than 100.
-
-
-
-**BamTools Header:**
-
-**BamTools Header Command**
-
-``` syntaxhighlighter-pre
- bamtools header -in input_alignments.bam -out output_alignments_header.txt
-```
-
-The command **bamtools header** prints the header from BAM file.
-
-
-
-**BamTools Index:**
-
-**BamTools Index Command**
-
-``` syntaxhighlighter-pre
- bamtools index -in input_alignments.bam
-```
-
-The command **bamtools index** creates index for BAM file and prints
-**input\_alignments.bam.bai** file.
-
-
-
-**BamTools Merge:**
-
-**BamTools Merge Command**
-
-``` syntaxhighlighter-pre
- bamtools merge -in input_alignments_1.bam -in input_alignments_2.bam -in input_alignments_3.bam -out output_alignments_merged.bam
-```
-
-The command **bamtools merge** merges multiple (more than 2) BAM files
-into one.
-
-
-
-**BamTools Random:**
-
-**BamTools Random Command**
-
-``` syntaxhighlighter-pre
- bamtools random -in input_alignments.bam -out output_alignments_100.bam -n 100
-```
-
-The command **bamtools random** grabs a random subset of alignments.
-With the option **-n 100**, 100 randomly chosen alignments are stored in
-the output file **output\_alignments\_100.bam**.
-
-
-
-**BamTools Resolve:**
-
-**BamTools Resolve Command**
-
-``` syntaxhighlighter-pre
- bamtools resolve -twoPass -in input_alignments.bam -out output_alignments.bam
-```
-
-The command **bamtools resolve** resolves paired-end reads. The
-resolving mode is required, and it can be **-makeStats**,
-**-markPairs**, or **-twoPass**.
-
-**
-**
-
-**BamTools Revert:**
-
-**BamTools Revert Command**
-
-``` syntaxhighlighter-pre
- bamtools revert -in input_alignments.bam -out output_alignments_reverted.bam
-```
-
-The command **bamtools revert** removes duplicate marks and restores
-original base qualities.
-
-
-
-**BamTools Sort:**
-
-**BamTools Sort Command**
-
-``` syntaxhighlighter-pre
- bamtools sort -in input_alignments.bam -out output_alignments_sorted.bam -byname
-```
-
-The command **bamtools sort** sorts a BAM file according to a given
-option. **Output\_alignments\_sorted.bam** is the resulting file, where
-the alignments are sorted by name.
-
-
-
-**BamTools Split:**
-
-**BamTools Split Command**
-
-``` syntaxhighlighter-pre
- bamtools split -in input_alignments.bam -mapped
-```
-
-The command **bamtools split** splits BAM file on user-specified
-property and creates a new BAM output file for each value found. In the
-given example, an output file **input\_alignments.MAPPED.bam** is
-produced after -**mapped** split option is specified. Beside **mapped**,
-the split option can be: **-paired**, **-reference**, or **-tag
-<tag\_name>**.
-
-
-
-**BamTools Stats:**
-
-**BamTools Stats Command**
-
-``` syntaxhighlighter-pre
- bamtools stats -in input_alignments.bam
-```
-
-The command **bamtools stats** prints general alignment statistics from
-the BAM file.
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_bamtools\_module.xsl](attachments/8193306/8127595.xsl)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193306/8127596.xml)
-(application/octet-stream)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325460.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325486.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325505.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325538.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325875.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325894.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325922.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325941.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325972.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326030.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326101.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326214.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326316.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326410.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326438.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326506.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326556.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326595.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326646.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326668.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326826.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326903.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326938.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35326957.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35327039.xml) (text/xml)
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[hcc\_modules.xml](attachments/8193306/35325387.xml) (text/xml)
-
-
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md
new file mode 100644
index 0000000000000000000000000000000000000000..c363f7798fda505369e6f4fa2c3f9f6cafb114d4
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md
@@ -0,0 +1,89 @@
++++
+title = "Running SAMtools Commands"
+description = "How to run SAMtools commands on HCC resources"
+weight = "10"
++++
+
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">SAMtools View:</span>
+
+One of the most frequently used SAMtools command is **view**. The basic usage of the **samtools view** is:
+{{< highlight bash >}}
+$ samtools view input_alignments.[bam|sam] [options] -o output_alignments.[sam|bam]
+{{< /highlight >}}
+where **input_alignments.[bam|sam]** is the input file with the alignments in BAM/SAM format, and **output_alignments.[sam|bam]** file is the converted file into SAM or BAM format respectively.
+
+Running **samtools view** on Tusker with `8 CPUs`, input file `input_alignments.sam` with available header (**-S**), output in BAM format (**-b**) and output file `output_alignments.bam` is shown below:
+{{% panel header="`samtools_view.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=SAMtools_View
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=SAMtools.%J.out
+#SBATCH --error=SAMtools.%J.err
+
+module load samtools/1.9
+
+samtools view -bS -@ $SLURM_NTASKS_PER_NODE input_alignments.sam -o output_alignments.bam
+{{< /highlight >}}
+{{% /panel %}}
+
+The most intensive SAMtools commands (**samtools view**, **samtools sort**) are multi-threaded, and therefore using the SAMtools option **-@ <number_of_CPUs>** is recommended.
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">SAMtools Sort:</span>
+
+Sorting BAM files is recommended for further analysis of these files. The BAM file is sorted based on its position in the reference, as determined by its alignment. An example of using `4 CPUs` to sort the input file `input_alignments.bam` by the read name follows:
+{{< highlight bash >}}
+$ samtools sort -n -@ 4 input_alignments.bam output_alignments_sorted
+{{< /highlight >}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">SAMtools Index:</span>
+
+The **samtools index** command creates a new index file that allows fast look-up of the data in a sorted SAM or BAM file.
+{{< highlight bash >}}
+$ samtools index input_alignments_sorted.bam output_index.bai
+{{< /highlight >}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">SAMtools Idxstats:</span>
+
+The **samtools idxstats** command prints stats for the BAM index file. The output is TAB delimited with each line consisting of *reference sequence name*, *sequence length*, *number of mapped reads* and *number of unmapped reads*.
+{{< highlight bash >}}
+$ samtools idxstats input_alignments_sorted.bam
+{{< /highlight >}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">SAMtools Merge:</span>
+
+The **samtools merge** command merges multiple sorted alignments into one output file.
+{{< highlight bash >}}
+$ samtools merge output_alignments_merge.bam input_alignments_sorted_1.bam input_alignments_sorted_2.bam
+{{< /highlight >}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">SAMtools Faidx:</span>
+
+The command **samtools faidx** indexes the reference sequence in fasta format or extracts subsequence from indexed reference sequence.
+{{< highlight bash >}}
+$ samtools faidx input_reference.fasta
+{{< /highlight >}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">SAMtools Mpileup:</span>
+
+The **samtools mpileup** command generates file in `bcf` or `pileup` format for one or multiple BAM files. For each genomic coordinate, the overlapping read bases and indels at that position in the input BAM file are printed.
+{{< highlight bash >}}
+$ samtools mpileup input_alignments_sorted.bam > output_alignments.bcf
+{{< /highlight >}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">SAMtools View:</span>
+
+The **samtools tview** command starts an interactive text alignment viewer that can be used to visualize how reads are aligned to specific regions of the reference genome.
+{{< highlight bash >}}
+$ samtools tview input_alignments_sorted.bam
+{{< /highlight >}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/sratoolkit.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/sratoolkit.md
new file mode 100644
index 0000000000000000000000000000000000000000..cdf537ef8e9698d790f4dac5d832c2b7273a36a1
--- /dev/null
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/sratoolkit.md
@@ -0,0 +1,81 @@
++++
+title = "SRAtoolkit"
+description = "How to run SRAtoolkit on HCC resources"
+weight = "10"
++++
+
+
+[SRA (Sequence Read Archive)] (http://www.ncbi.nlm.nih.gov/sra) is an NCBI-defined format for NGS data. Every data submitted to NCBI needs to be in SRA format. The SRA Toolkit provides tools for converting different formats of data into SRA format, and vice versa, extracting SRA data in other different formats.
+
+The SRA Toolkit allows converting data from the SRA format to the following formats: `ABI SOLiD native`, `fasta`, `fastq`, `sff`, `sam`, and `Illumina native`. Also, the SRA Toolkit allows converting data from `fasta`, `fastq`, `AB SOLiD-SRF`, `AB SOLiD-native`, `Illumina SRF`, `Illumina native`, `sff`, and `bam` format into the SRA format.
+
+The SRA Toolkit contains multiple **"format"-dump** commands, where **format** is the file format the SRA data is converted to **abi-dump**, **fastq-dump**, **illumina-dump**, **sam-dump**, **sff-dump**, and **vdb-dump**.
+
+One of the most commonly used commands is **fastq-dump**:
+{{< highlight bash >}}
+$ fastq-dump [options] input_reads.sra
+{{< /highlight >}}
+
+\\
+An example of running **fastq-dump** on Tusker to convert SRA file containing paired-end reads is:
+{{% panel header="`sratoolkit.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=SRAtoolkit
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=SRAtoolkit.%J.out
+#SBATCH --error=SRAtoolkit.%J.err
+
+module load SRAtoolkit/2.9
+
+fastq-dump --split-files input_reads.sra
+{{< /highlight >}}
+{{% /panel %}}
+This script outputs two fastq paired end reads `input_reads_1.fastq` and `input_reads_2.fastq`.
+
+All SRAtoolkit commands are single threaded, and therefore both `#SBATCH --nodes` and `#SBATCH --ntasks-per-node` in the SLURM script are set to **1**.
+
+\\
+The SRA Toolkit contains multiple **"format"-load** commands, where **format** is the file format of the data that is uploaded to NCBI: `srf-load`, `sff-load`, `refseq-load`, `pacbio-load`, `illumina-load`, `helicos-load`, `fastq-load`, `cg-load`, `bam-load`, and `abi-load`.
+
+An example of bam file `input_alignments.bam` uploaded to NCBI is shown below:
+{{< highlight bash >}}
+$ bam-load \-o input_reads.sra input_alignments.bam
+{{< /highlight >}}
+
+\\
+Other frequently used SRAtoolkit tools are:
+
+- **prefetch**: allows command-line downloading of SRA, dbGaP, and ADSP data
+- **sra-stat**: generate statistics about SRA data
+- **sra-pileup**: generate pileup statistics on aligned SRA data
+- **vdb-config**: display and modify VDB configuration information
+- **vdb-encrypt**: encrypt non-SRA dbGaP data
+- **vdb-decrypt**: decrypt non-SRA dbGaP data
+- **vdb-validate**: validate the integrity of downloaded SRA data
+
+{{% notice info %}}
+**Prefetch instructions:**
+\\
+\\
+When **prefetch** is used, the files are downloaded in **${HOME}/ncbi/public** by default.
+\\
+Since the */home* directory (*$HOME*) is not writable from the worker nodes, the file can not be saved in *$(HOME)/ncbi/public* when submitting a SLURM job.
+\\
+\\
+To change the default output directory for **prefetch** to **${WORK}/ncbi/public**, please follow these three steps:
+\\
+**$ wget https://raw.githubusercontent.com/ncbi/ncbi-vdb/master/libs/kfg/default.kfg -P $HOME/.ncbi/**
+\\
+**$ vim $HOME/.ncbi/default.kfg**
+\\
+Here, set *"/repository/user/main/public/root"* to *"/work/group/username/ncbi/public"*, where **group** is the name of **your HCC group**, and **username** is **your HCC username**.
+\\
+**$ export VDB_CONFIG=$HOME/.ncbi/default.kfg**
+\\
+\\
+You need to do these steps only once.
+{{% /notice %}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/oases.md b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/oases.md
index 676ecec7c9e0694016a67de52674d89cd4e1a74c..9cfbcc1c8e36b74ac44fdae30ca83f3aaf060cc9 100644
--- a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/oases.md
+++ b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/oases.md
@@ -35,7 +35,7 @@ A simple SLURM script to run Oases on the Velvet output stored in `output_direct
#SBATCH --output=Oases.%J.out
#SBATCH --error=Oases.%J.err
-module load oases/0.2.8
+module load oases/0.2
oases output_directory/ -min_trans_lgth 200
{{< /highlight >}}
diff --git a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/ray.md b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/ray.md
index 15c809732171679db5b8d4c09dd98c5884a2d73a..485937885ba7ba358e4e1b61658518fdf4cf9f11 100644
--- a/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/ray.md
+++ b/content/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/ray.md
@@ -54,7 +54,7 @@ mpiexec Ray -k 31 -p input_reads_pair_1.fastq input_reads_pair_2.fastq -s input_
{{% /panel %}}
where **input_reads_pair_1.fastq** and **input_reads_pair_2.fastq** are the paired-end input files in `fastq` format, and **input_reads.fasta** is the single-end input file in `fasta` format.
-{{% notice tip %}}
+{{% notice note %}}
It is **not** necessary to specify the number of processes with the `-n` option to `mpiexec`. OpenMPI will determine that automatically from SLURM based on the value of the `--ntasks` option.
{{% /notice %}}
diff --git a/static/html/blast.html b/static/html/blast.html
new file mode 100644
index 0000000000000000000000000000000000000000..72a7555d8e8f09d58d8d249623d0768b0c349fd8
--- /dev/null
+++ b/static/html/blast.html
@@ -0,0 +1,50 @@
+ <table style="font-size: small">
+ <colgroup>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ </colgroup>
+ <tbody>
+ <tr style="font-size: x-small">
+ <th></th>
+ <th>total # of sequences</th>
+ <th>total # of bases</th>
+ <th>total size in MB</th>
+ <th>used time</th>
+ <th>used memory</th>
+ <th># of used CPUs</th>
+ </tr>
+
+ <tr>
+ <td colspan="1"><strong>small.fasta</strong></td>
+ <td colspan="1">41,715</td>
+ <td colspan="1">35,581,740</td>
+ <td colspan="1">37.627 </td>
+ <td colspan="1">~ 2 hours</td>
+ <td colspan="1">~ 23 GB</td>
+ <td colspan="1">8</td>
+ </tr>
+ <tr>
+ <td colspan="1"><strong>medium.fasta</strong></td>
+ <td colspan="1">110,478</td>
+ <td colspan="1">147,543,113</td>
+ <td colspan="1">149 </td>
+ <td colspan="1">~ 4 hours</td>
+ <td colspan="1">~ 24 GB</td>
+ <td colspan="1">8</td>
+ </tr>
+ <tr>
+ <td colspan="1"><strong>large.fasta</strong></td>
+ <td colspan="1">592,593</td>
+ <td colspan="1">827,629,204</td>
+ <td colspan="1">836</td>
+ <td colspan="1">~ 15 hours</td>
+ <td colspan="1">~ 47 GB</td>
+ <td colspan="1">8</td>
+ </tr>
+ </tbody>
+ </table>
\ No newline at end of file
diff --git a/static/html/bwa.html b/static/html/bwa.html
new file mode 100644
index 0000000000000000000000000000000000000000..e7b9c4d4723eee767e2c855ec22801d0a863d827
--- /dev/null
+++ b/static/html/bwa.html
@@ -0,0 +1,66 @@
+ <table style="font-size: small">
+ <colgroup>
+ <col style="width: 8.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ </colgroup>
+ <tbody>
+ <tr style="font-size: x-small">
+ <th></th>
+ <th>total # of sequences</th>
+ <th>total size in MB</th>
+ <th># of used CPUs</th>
+ <th>used time for 4 CPUs</th>
+ <th>used memory for 4 CPUs</th>
+ <th># of used CPUs</th>
+ <th>used time for 8 CPUs</th>
+ <th>used memory for 8 CPUs</th>
+ <th># of used CPUs</th>
+ <th>used time for 16 CPUs</th>
+ <th>used memory for 16 CPUs</th>
+ </tr>
+
+ <tr>
+ <td colspan="1"><strong>large_1.fastq</strong></td>
+ <td colspan="1">10,174,715</td>
+ <td colspan="1">3,376</td>
+ <td colspan="1" rowspan="2">4</td>
+ <td colspan="1" rowspan="2">~ 35 minutes</td>
+ <td colspan="1" rowspan="2">~ 12 GB</td>
+ <td colspan="1" rowspan="2">8</td>
+ <td colspan="1" rowspan="2">~ 18.5 minutes</td>
+ <td colspan="1" rowspan="2">~ 18 GB</td>
+ <td colspan="1" rowspan="2">16</td>
+ <td colspan="1" rowspan="2">~ 10 minutes</td>
+ <td colspan="1" rowspan="2">~ 19 GB</td>
+ </tr>
+ <tr>
+ <td colspan="1"><strong>large_2.fastq</strong></td>
+ <td colspan="1">10,174,715</td>
+ <td colspan="1">3,376 </td>
+ </tr>
+ <tr>
+ <td colspan="1"><strong>large.fasta</strong></td>
+ <td colspan="1">592,593</td>
+ <td colspan="1">836</td>
+ <td colspan="1" rowspan="2">4</td>
+ <td colspan="1" rowspan="2">~ 5.5 minutes</td>
+ <td colspan="1" rowspan="2">~ 3 GB</td>
+ <td colspan="1" rowspan="2">8</td>
+ <td colspan="1" rowspan="2">~ 3 minutes</td>
+ <td colspan="1" rowspan="2">~ 4 GB</td>
+ <td colspan="1" rowspan="2">16</td>
+ <td colspan="1" rowspan="2">~ 2 minutes</td>
+ <td colspan="1" rowspan="2">~ 6.2 GB</td>
+ </tr>
+ </tbody>
+ </table>
\ No newline at end of file
diff --git a/static/html/clustal_omega.html b/static/html/clustal_omega.html
new file mode 100644
index 0000000000000000000000000000000000000000..aa2bfd1cde859da781db3b28043b8b1e8e60a279
--- /dev/null
+++ b/static/html/clustal_omega.html
@@ -0,0 +1,50 @@
+ <table style="font-size: small">
+ <colgroup>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ <col style="width: 6.80757%;"/>
+ </colgroup>
+ <tbody>
+ <tr style="font-size: x-small">
+ <th></th>
+ <th>total # of sequences</th>
+ <th>average sequence length</th>
+ <th>total size</th>
+ <th>used time</th>
+ <th>used memory</th>
+ <th># of used CPUs</th>
+ </tr>
+
+ <tr>
+ <td colspan="1"><strong>data_1.fasta</strong></td>
+ <td colspan="1">1,200</td>
+ <td colspan="1">510.17</td>
+ <td colspan="1">641 KB</td>
+ <td colspan="1">~ 5 minutes</td>
+ <td colspan="1">~ 65 MB</td>
+ <td colspan="1">8</td>
+ </tr>
+ <tr>
+ <td colspan="1"><strong>data_2.fasta</strong></td>
+ <td colspan="1">5,715</td>
+ <td colspan="1">174.20</td>
+ <td colspan="1">1,100 KB</td>
+ <td colspan="1">~ 5 minutes</td>
+ <td colspan="1">~ 140 MB</td>
+ <td colspan="1">8</td>
+ </tr>
+ <tr>
+ <td colspan="1"><strong>data_3.fasta</strong></td>
+ <td colspan="1">93,675</td>
+ <td colspan="1">94.29</td>
+ <td colspan="1">11,000 KB</td>
+ <td colspan="1">~ 30 minutes</td>
+ <td colspan="1">~ 2 GB</td>
+ <td colspan="1">8</td>
+ </tr>
+ </tbody>
+ </table>
\ No newline at end of file
diff --git a/static/html/trinity.html b/static/html/trinity.html
index 928574aa98933a78ef316c81be4b510663ef39d3..a3edf302f3cbda8fa667dbbb6e731857d015e5fc 100644
--- a/static/html/trinity.html
+++ b/static/html/trinity.html
@@ -1,7 +1,8 @@
<table style="font-size: small">
<colgroup>
- <col style="width: 6.80757%;"/>
- <col style="width: 6.80757%;"/>
+ <col style="width: 10.80757%;"/>
+ <col style="width: 7.80757%;"/>
+ <col style="width: 9.80757%;"/>
<col style="width: 6.80757%;"/>
<col style="width: 6.80757%;"/>
<col style="width: 6.80757%;"/>
diff --git a/static/html/velvet.html b/static/html/velvet.html
index b8edb9e93777c163a7865991e249f3b3aef6f412..f7b22a96e09c57197900c627bdc83dcf0eb04713 100644
--- a/static/html/velvet.html
+++ b/static/html/velvet.html
@@ -1,7 +1,8 @@
<table style="font-size: small">
<colgroup>
- <col style="width: 6.80757%;"/>
- <col style="width: 6.80757%;"/>
+ <col style="width: 10.80757%;"/>
+ <col style="width: 7.80757%;"/>
+ <col style="width: 9.80757%;"/>
<col style="width: 6.80757%;"/>
<col style="width: 6.80757%;"/>
<col style="width: 6.80757%;"/>