From fec3463739e3e596fa8101ea3323cc6ee76301e8 Mon Sep 17 00:00:00 2001
From: npavlovikj <npavlovikj2@unl.edu>
Date: Wed, 14 Nov 2018 17:47:52 -0600
Subject: [PATCH] add bioinformatics pages part 2

---
 .../biodata_module/_index.md                  |    2 +-
 .../pre_processing_tools/_index.md            |   19 +-
 .../pre_processing_tools/cutadapt.md          |  160 +-
 .../pre_processing_tools/prinseq.md           |  201 +-
 .../pre_processing_tools/scythe.md            |  228 +-
 .../pre_processing_tools/sickle.md            |  317 +-
 .../pre_processing_tools/tagcleaner.md        |  137 +-
 .../bioinformatics_tools/qiime.md             |    1 +
 .../reference_based_assembly_tools/_index.md  |   19 +-
 .../cufflinks.md                              | 2911 +----------------
 .../_index.md                                 |   19 +-
 .../cap3.md                                   |  199 +-
 .../cd_hit.md                                 |  160 +-
 static/html/cap3.html                         |   50 +
 static/html/scythe.html                       |   77 +
 static/html/sickle.html                       |   68 +
 16 files changed, 657 insertions(+), 3911 deletions(-)
 create mode 100644 static/html/cap3.html
 create mode 100644 static/html/scythe.html
 create mode 100644 static/html/sickle.html

diff --git a/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md b/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
index 91fa2544..8d1fcfa7 100644
--- a/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
@@ -46,6 +46,7 @@ An example of how to run Bowtie2 local alignment on Crane utilizing the default
 
 module load bowtie/2.2
 module load biodata
+
 bowtie2 -x $BOWTIE2_HORSE -f -1 input_reads_pair_1.fasta -2 input_reads_pair_2.fasta -S bowtie2_alignments.sam --local -p $SLURM_NTASKS_PER_NODE
 
 {{< /highlight >}}
@@ -76,4 +77,3 @@ cp /scratch/blast_nucleotide.results .
   
 The organisms and their appropriate environmental variables for all genomes and chromosome files, as well as for short read aligned indices are shown on the link below:  
 [Organisms](#organisms)
-
diff --git a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/_index.md b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/_index.md
index 42a2850c..7e446783 100644
--- a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/_index.md
@@ -1,14 +1,7 @@
-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 : Pre-Processing Tools </span>
-==============================================================
-
-Created by <span class="author"> Adam Caprez</span> on Sep 04, 2014
-
- 
-
++++
+title = "Pre-processing Tools"
+description = "How to use pre-processing tools on HCC machines"
+weight = "52"
++++
 
+{{% children %}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/cutadapt.md b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/cutadapt.md
index 1c3dbdc6..ae0d820b 100644
--- a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/cutadapt.md
+++ b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/cutadapt.md
@@ -1,119 +1,53 @@
-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.  [Pre-Processing Tools](Pre-Processing-Tools_8193298.html)
++++
+title = "Cutadapt"
+description =  "How to run Cutadapt on HCC resources"
+weight = "10"
++++
 
-<span id="title-text"> HCC-DOCS : Cutadapt </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 |
-|----------|---------|----------|
-| cutadapt | 1.4     | Tusker   |
-
-|          |     |       |
-|----------|-----|-------|
-| cutadapt | 1.4 | Crane |
-
- 
-
-Cutadapt
-(<a href="https://code.google.com/p/cutadapt/" class="external-link">https://code.google.com/p/cutadapt/</a>)
-is a tool for removing adapter sequences from DNA sequencing data.
-Although most of the adapters are located at the 3' end of the
-sequencing read, Cutadapt allows multiple adapter removal from both 3'
-and 5' ends.
+[Cutadapt] (https://cutadapt.readthedocs.io/en/stable/index.html) is a tool for removing adapter sequences from DNA sequencing data. Although most of the adapters are located at the 3' end of the sequencing read, Cutadapt allows multiple adapter removal from both 3' and 5' ends.
 
 The basic usage of Cutadapt is:
+{{< highlight bash >}}
+$ cutadapt [-a|-b|-g] <adapter_sequence> input_reads.[fasta|fastq] > output_reads.[fasta|fastq]
+{{< /highlight >}}
 
-**General Cutadapt Usage**
-
-``` syntaxhighlighter-pre
-cutadapt [-a|-b|-g] <adapter_sequence> input_reads.[fasta|fastq] > output_reads.[fasta|fastq]
-```
-
-where **&lt;adapter\_sequence&gt;** is the nucleotide sequence of the
-actual adapter, i**nput\_reads.\[fasta\|fastq\]** is the input file with
-sequencing data in fasta/fastq format, and respectively,
-**output\_reads.\[fasta\|fastq\]** is the final trimmed file in
-fasta/fastq format. The option **-a** allows removing of an adapter from
-the 3' end of the sequencing read. The option **-b** removes adapters
-ligated to the 5' or 3' end. The option **-g** removes adapter sequences
-from the 5' end. These options can be used multiple times for different
-adapters.
+where **&lt;adapter_sequence&gt;** is the nucleotide sequence of the actual adapter, **input_reads.[fasta|fastq]** is the input file with sequencing data in fasta/fastq format, and respectively, **output_reads.[fasta|fastq]** is the final trimmed file in fasta/fastq format.
+\\
+The option **-a** allows removal of adapters from the 3' end of the sequencing read. The option **-b** removes adapters ligated to the 5' or 3' end. The option **-g** removes adapter sequences from the 5' end. These options can be used multiple times for different adapters.
 
 More information about the Cutadapt options can be found by typing:
-
-**Additional Cutadapt Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.tusker~]$ cutadapt --help
-```
-
-Simple Cutadapt script that trims the adapter sequences **AGGCACACAGGG**
-and **TGAGACACGCA** from the 3' end and **AACCGGTT** from the 5' end of
-single-end fasta input file is shown below:
-
-**cutadapt.submit**
-
-\#!/bin/sh  
-\#SBATCH --job-name=Cutadapt  
-\#SBATCH --nodes=1  
-\#SBATCH --ntasks-per-node=1  
-\#SBATCH --time=168:00:00  
-\#SBATCH --mem=30gb  
-\#SBATCH --output=Cutadapt.%J.out  
-\#SBATCH --error=Cutadapt.%J.err
-
- 
-
-|                                     |
-|-------------------------------------|
-| module load python/2.7 cutadapt/1.4 |
-
-cutadapt -a AGGCACACAGGG -a TGAGACACGCA -g AACCGGTT input\_reads.fasta
-&gt; output\_reads.fasta
-
-Cutadapt is single threaded program, and therefore **\#SBATCH
---nodes=1** and **\#SBATCH --ntasks-per-node=1**. Cutadapt allows
-paired-end trimming where each pair is trimmed separately in a single
-pass:
-
-**Cutadapt Usage for Paired-End Reads**
-
-``` syntaxhighlighter-pre
-cutadapt -a ADAPTER_PAIR_1 input_reads_pair_1.fastq > output_reads_pair_1.fastq
-cutadapt -a ADAPTER_PAIR_2 input_reads_pair_2.fastq > output_reads_pair_2.fastq
-```
-
- 
-
-**Cutadapt Output**
-
-Beside the fasta/fastq file of reads with removed adapter sequences,
-Cutadapt also outputs useful statistics per adapter sequence.
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_cutadapt\_module.xsl](attachments/8193303/8127586.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_cutadapt\_version.xsl](attachments/8193303/8127587.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193303/8127588.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_cutadapt\_version.xsl](attachments/8193303/8127589.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193303/8127590.xml)
-(application/octet-stream)  
-
-
+{{< highlight bash >}}
+$ cutadapt --help
+{{< /highlight >}}
+\\
+Simple Cutadapt script that trims the adapter sequences **AGGCACACAGGG** and **TGAGACACGCA** from the 3' end and **AACCGGTT** from the 5' end of single-end fasta input file is shown below:
+{{% panel header="`cutadapt.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=Cutadapt
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=Cutadapt.%J.out
+#SBATCH --error=Cutadapt.%J.err
+
+module load cutadapt/1.13
+
+cutadapt -a AGGCACACAGGG -a TGAGACACGCA -g AACCGGTT input_reads.fasta > output_reads.fasta
+{{< /highlight >}}
+{{% /panel %}}
+
+Cutadapt is single threaded program, and therefore `#SBATCH --nodes=1` and `#SBATCH --ntasks-per-node=1`.
+\\
+\\
+\\
+Cutadapt allows paired-end trimming where each pair is trimmed separately in a single pass:
+{{< highlight bash >}}
+$ cutadapt -a ADAPTER_PAIR_1 input_reads_pair_1.fastq > output_reads_pair_1.fastq
+$ cutadapt -a ADAPTER_PAIR_2 input_reads_pair_2.fastq > output_reads_pair_2.fastq
+{{< /highlight >}}
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Cutadapt Output</span>
+
+Beside the fasta/fastq file of reads with removed adapter sequences, Cutadapt also outputs useful statistics per adapter sequence.
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/prinseq.md b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/prinseq.md
index ecd49da5..70dde83f 100644
--- a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/prinseq.md
+++ b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/prinseq.md
@@ -1,150 +1,79 @@
-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.  [Pre-Processing Tools](Pre-Processing-Tools_8193298.html)
++++
+title = "PRINSEQ"
+description =  "How to run PRINSEQ on HCC resources"
+weight = "10"
++++
 
-<span id="title-text"> HCC-DOCS : PRINSEQ </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 |
-|--------------|---------|----------|
-| prinseq-lite | 0.20    | Crane    |
-
- 
-
-PRINSEQ (PReprocessing and INformation of SEQuence data)
-(<a href="http://prinseq.sourceforge.net/" class="external-link">http://prinseq.sourceforge.net/</a>)
-is a tool used for filtering, formatting or trimming genome and
-metagenomic sequence data in fasta/fastq format. Moreover, PRINSEQ
-generates summary statistics of sequence and quality data.
+[PRINSEQ (PReprocessing and INformation of SEQuence data)] (http://prinseq.sourceforge.net/) is a tool used for filtering, formatting or trimming genome and metagenomic sequence data in fasta/fastq format. Moreover, PRINSEQ generates summary statistics of sequence and quality data.
 
 More information about the PRINSEQ program can be shown with:
-
-**Additional PRINSEQ Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.crane ~]$  prinseq-lite.pl --help
-```
-
-**  
-**
-
-**PRINSEQ script for single-end fasta data**
+{{< highlight bash >}}
+$ prinseq-lite.pl --help
+{{< /highlight >}}
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">PRINSEQ with single-end fasta data</span>
 
 The basic usage of PRINSEQ for single-end data is:
-
-**General PRINSEQ Usage for Single-End Data**
-
-``` syntaxhighlighter-pre
-prinseq-lite.pl [-fasta|-fastq] input_reads.[fasta|fastq] -out_format [1|2|3|4|5] [options]
-```
-
-where **input\_reads.\[fasta\|fastq\]** is an input file of sequence
-data in fasta/fastq format, and **options** are additional parameters
-that can be found in the PRINSEQ manual:
-<a href="http://prinseq.sourceforge.net/manual.html" class="external-link">http://prinseq.sourceforge.net/manual.html</a>.
-The output format (**-out\_format**) can be **1 **(fasta only),
-**2 **(fasta and qual), **3 **(fastq), **4 **(fastq and input fasta),
-and **5 **(fastq, fasta and qual).
-
-Simple PRINSEQ SLURM script for single-end fasta data and fasta output
-format is shown below:
-
-**prinseq\_single\_end.submit**
-
-\#!/bin/sh  
-\#SBATCH --job-name=PRINSEQ  
-\#SBATCH --nodes=1  
-\#SBATCH --ntasks-per-node=1  
-\#SBATCH --time=168:00:00  
-\#SBATCH --mem=20gb  
-\#SBATCH --output=PRINSEQ\_single.%J.out  
-\#SBATCH --error=PRINSEQ\_single.%J.err
-
- 
-
-|                               |
-|-------------------------------|
-| module load prinseq-lite/0.20 |
-
-prinseq-lite.pl -fasta input\_reads.fasta -out\_format 1
-
-PRINSEQ is single threaded program, and therefore both **\#SBATCH
---nodes** and **\#SBATCH --ntasks-per-node** are set to **1**.
-
- 
-
-**PRINSEQ script for paired-end fastq data**
+{{< highlight bash >}}
+$ prinseq-lite.pl [-fasta|-fastq] input_reads.[fasta|fastq] -out_format [1|2|3|4|5] [options]
+{{< /highlight >}}
+where **input_reads.[fasta|fastq]** is an input file of sequence data in fasta/fastq format, and **options** are additional parameters that can be found in the [PRINSEQ manual] (http://prinseq.sourceforge.net/manual.html).
+
+The output format (`-out_format`) can be **1** (fasta only), **2** (fasta and qual), **3** (fastq), **4** (fastq and input fasta), and **5** (fastq, fasta and qual).
+
+Simple PRINSEQ SLURM script for single-end fasta data and fasta output format is shown below:
+{{% panel header="`prinseq_single_end.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=PRINSEQ
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=PRINSEQ_single.%J.out
+#SBATCH --error=PRINSEQ_single.%J.err
+
+module load prinseq-lite/0.20
+
+prinseq-lite.pl -fasta input_reads.fasta -out_format 1
+{{< /highlight >}}
+{{% /panel %}}
+
+PRINSEQ is single threaded program, 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;">PRINSEQ for paired-end fastq data</span>
 
 The basic usage of PRINSEQ for paired-end data is:
+{{< highlight bash >}}
+$ prinseq-lite.pl [-fasta|-fastq] input_reads_pair_1.[fasta|fastq] [-fasta2|-fastq2] input_reads_pair_2.[fasta|fastq] -out_format [1|2|3|4|5] [options]
+{{< /highlight >}}
+where **input_reads_pair_1.[fasta|fastq]** and **input_reads_pair_2.[fasta|fastq]** are pair 1 and pair 2 of the input files of sequence data in fasta/fastq format, and **options** are additional parameters that can be found in the the [PRINSEQ manual] (http://prinseq.sourceforge.net/manual.html).
 
-**General PRINSEQ Usage for Paired-End Data**
-
-``` syntaxhighlighter-pre
-prinseq-lite.pl [-fasta|-fastq] input_reads_pair_1.[fasta|fastq] [-fasta2|-fastq2] input_reads_pair_2.[fasta|fastq] -out_format [1|2|3|4|5] [options]
-```
-
-where **input\_reads\_pair\_1.\[fasta\|fastq\]**
-and ****input\_reads\_pair\_2.\[fasta\|fastq\]**** are pair 1 and pair 2
-of the input files of sequence data in fasta/fastq format,
-and **options** are additional parameters that can be found in the
-PRINSEQ
-manual: <a href="http://prinseq.sourceforge.net/manual.html" class="external-link">http://prinseq.sourceforge.net/manual.html</a>.
-The output format (**-out\_format**) can be **1 **(fasta only),
-**2 **(fasta and qual), **3 **(fastq), **4 **(fastq and input fasta),
-and **5 **(fastq, fasta and qual).
-
-Simple PRINSEQ SLURM script for paired-end fastq data and fastq output
-format is shown below:
-
-**prinseq\_paired\_end.submit**
-
-\#!/bin/sh  
-\#SBATCH --job-name=PRINSEQ  
-\#SBATCH --nodes=1  
-\#SBATCH --ntasks-per-node=1  
-\#SBATCH --time=168:00:00  
-\#SBATCH --mem=20gb  
-\#SBATCH --output=PRINSEQ\_paired.%J.out  
-\#SBATCH --error=PRINSEQ\_paired.%J.err
-
- 
-
-|                               |
-|-------------------------------|
-| module load prinseq-lite/0.20 |
-
-prinseq-lite.pl -fastq input\_reads\_pair\_1.fastq -fastq2
-input\_reads\_pair\_2.fastq -out\_format 3
-
-PRINSEQ is single threaded program, and therefore both **\#SBATCH
---nodes** and **\#SBATCH --ntasks-per-node** are set to **1**.
-
-**  
-**
+The output format (`-out_format`) can be **1** (fasta only), **2** (fasta and qual), **3** (fastq), **4** (fastq and input fasta), and **5** (fastq, fasta and qual).
 
-**PRINSEQ Output**
+Simple PRINSEQ SLURM script for paired-end fastq data and fastq output format is shown below:
+{{% panel header="`prinseq_paired_end.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=PRINSEQ
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=PRINSEQ_paired.%J.out
+#SBATCH --error=PRINSEQ_paired.%J.err
 
-PRINSEQ gives statistics about the input and filtered sequences, and
-also outputs single-end or paired-end files of sequences filtered by
-specified parameters.
+module load prinseq-lite/0.20
 
-Attachments:
-------------
+prinseq-lite.pl -fastq input_reads_pair_1.fastq -fastq2 input_reads_pair_2.fastq -out_format 3
+{{< /highlight >}}
+{{% /panel %}}
 
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_prinseq\_module.xsl](attachments/8193299/8127572.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193299/8127573.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_prinseq\_version.xsl](attachments/8193299/8127574.xsl)
-(application/octet-stream)  
+PRINSEQ is single threaded program, 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;">PRINSEQ Output</span>
 
+PRINSEQ gives statistics about the input and filtered sequences, and also outputs files of single-end or paired-end sequences filtered by specified parameters.
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/scythe.md b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/scythe.md
index e0afc549..55240958 100644
--- a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/scythe.md
+++ b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/scythe.md
@@ -1,191 +1,55 @@
-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.  [Pre-Processing Tools](Pre-Processing-Tools_8193298.html)
++++
+title = "Scythe"
+description =  "How to run Scythe on HCC resources"
+weight = "10"
++++
 
-<span id="title-text"> HCC-DOCS : Scythe </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 |
-|--------|---------|----------|
-| scythe | 0.991   | Tusker   |
-
- 
-
-Scythe
-(<a href="https://github.com/vsbuffalo/scythe" class="external-link">https://github.com/vsbuffalo/scythe</a>)
-is a 3' end adapter trimmer that uses a Naive Bayesian approach to
-classify contaminant substrings in sequence reads. 3' ends often include
-poor quality bases which need to be removed prior the quality-based
-trimming, mapping, assemblies, and further analysis.
+[Scythe] (https://github.com/vsbuffalo/scythe) is a 3' end adapter trimmer that uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. 3' ends often include poor quality bases which need to be removed prior the quality-based trimming, mapping, assemblies, and further analysis.
 
 The basic usage of Scythe is:
+{{< highlight bash >}}
+$ scythe -a adapter_file.fasta input_reads.fastq -o output_reads.fastq
+{{< /highlight >}}
+where **adapter_file.fasta** is fasta input file of the adapter sequences that need to be removed from the 3' end of the sequence data, and **input_reads.fastq** is the input sequencing data in fastq format.
 
-**General Scythe Usage**
-
-``` syntaxhighlighter-pre
-scythe -a adapter_file.fasta input_reads.fastq -o output_reads.fastq
-```
-
-where **adapter\_file.fasta** is a fasta input file of the adapter
-sequences that need to be removed from the 3' end of the sequence data,
-and **input\_reads.fastq** is the input sequencing data in fastq format.
-The file **output\_reads.fastq** contains the sequencing reads with
-removed adapters. If the adapter sequences are unknown, Scythe by itself
-provides two adapter sequences that can be used with the **-a**
-option: **illumina\_adapters.fa** and **truseq\_adapters.fasta**.
+The file **output_reads.fastq** contains the sequencing reads with removed adapters. If the adapter sequences are unknown, Scythe by itself provides two adapter sequences that can be used with the **-a** option: **illumina_adapters.fa** and **truseq_adapters.fasta**.
 
 More information about Scythe can found by typing:
-
-**Additional Scythe Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.tusker ~]$ scythe --help
-```
-
-Simple Scythe script that uses the **illumina\_adapters.fa** file and
-**input\_reads.fastq** for Tusker is shown below:
-
-**scythe.submit**
-
-\#!/bin/sh  
-\#SBATCH --job-name=Scythe  
-\#SBATCH --nodes=1  
-\#SBATCH --ntasks-per-node=1  
-\#SBATCH --time=168:00:00  
-\#SBATCH --mem=20gb  
-\#SBATCH --output=Scythe.%J.out  
-\#SBATCH --error=Scythe.%J.err
-
- 
-
-|                          |
-|--------------------------|
-| module load scythe/0.991 |
-
-scythe -a $SCYTHE\_HOME/illumina\_adapters.fa input\_reads.fastq -o
-output\_reads.fastq
-
-Scythe is single threaded program, and therefore both **\#SBATCH
---nodes** and **\#SBATCH --ntasks-per-node** are set to **1**. The two
-adapter sequences provided by Scythe are stored in **$SCYTHE\_HOME**.
-Hence, to access the illumina adapter file
-use: **$SCYTHE\_HOME/illumina\_adapters.fa**, and to access the TruSeq
-file use:** $SCYTHE\_HOME/**truseq\_adapters.fasta****.
-
-**  
-**
-
-**Scythe Output**
+{{< highlight bash >}}
+$ scythe --help
+{{< /highlight >}}
+\\
+Simple Scythe script that uses the `illumina_adapters.fa` file and `input_reads.fastq` for Tusker is shown below:
+{{% panel header="`scythe.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=Scythe
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=Scythe.%J.out
+#SBATCH --error=Scythe.%J.err
+
+module load scythe/0.991
+
+scythe -a ${SCYTHE_HOME}/illumina_adapters.fa input_reads.fastq -o output_reads.fastq
+{{< /highlight >}}
+{{% /panel %}}
+
+Scythe is single threaded program, and therefore both `#SBATCH --nodes` and `#SBATCH --ntasks-per-node` are set to **1**. 
+
+The two adapter sequences provided by Scythe are stored in **$SCYTHE_HOME**. Hence, to access the illumina adapter file use: `$SCYTHE_HOME/illumina_adapters.fa`, and to access the TruSeq file use: `$SCYTHE_HOME/truseq_adapters.fasta`.
+\\
+\\
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Scythe Output</span>
 
 Scythe returns fastq file of reads with removed adapter sequences.
+\\
+\\
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Useful Information</span>
 
- 
-
-**Useful Information**
-
-In order to test the SCYTHE (scythe/0.991) performance on Tusker, we
-used three paired-end input fastq files: **small\_1.fastq**,
-**small\_2.fastq**, **medium\_1.fastq**, **medium\_2.fastq**,
-**large\_1.fastq, large\_2.fastq**. Some statistics about the input
-files and the time and memory resources required for SCYTHE 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>total # of bases</strong></p></th>
-<th><p><strong>total size in MB</strong></p></th>
-<th><p><strong>required time</strong></p></th>
-<th><p><strong>required memory</strong></p></th>
-<th># of used CPUs</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><p><strong>small_1.fastq</strong></p></td>
-<td><p>50,121</p></td>
-<td><p>2,506,050</p></td>
-<td><p>8.010 MB</p></td>
-<td><p>~ 0.04 minutes</p></td>
-<td><span>~ 0.014 GB</span></td>
-<td>1</td>
-</tr>
-<tr class="even">
-<td><p><strong>small_2.fastq</strong></p></td>
-<td><p>50,121</p></td>
-<td><p>2,506,050</p></td>
-<td><p>8.010 MB</p></td>
-<td><p>~ 0.04 minutes</p></td>
-<td><p>~ 0.014 GB</p></td>
-<td>1</td>
-</tr>
-<tr class="odd">
-<td><p><strong>medium_1.fastq</strong></p></td>
-<td><p>786,742</p></td>
-<td><p>59,792,392</p></td>
-<td><p>152 MB</p></td>
-<td><p>~ 1 minutes</p></td>
-<td><p><span>~ 0.2 GB</span></p></td>
-<td>1</td>
-</tr>
-<tr class="even">
-<td><p><strong>medium_2.fastq</strong></p></td>
-<td><p>786,742</p></td>
-<td><p>59,792,392</p></td>
-<td><p>152 MB</p></td>
-<td><p>~ 1 minutes</p></td>
-<td><p>~ 0.2 GB</p></td>
-<td>1</td>
-</tr>
-<tr class="odd">
-<td><p><strong>large_1.fastq</strong></p></td>
-<td><p>10,174,715</p></td>
-<td><p>1,027,646,215</p></td>
-<td><p>3,376 MB</p></td>
-<td>~ 13 minutes</td>
-<td><p>~ 3 GB</p></td>
-<td>1</td>
-</tr>
-<tr class="even">
-<td><p><strong>large_2.fastq</strong></p></td>
-<td><p>10,174,715</p></td>
-<td><p>1,027,646,215</p></td>
-<td><p>3,376 MB</p></td>
-<td>~ 17 minutes</td>
-<td><p>~ 6.5 GB</p></td>
-<td>1</td>
-</tr>
-</tbody>
-</table>
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_scythe\_module.xsl](attachments/8193301/8127578.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193301/8127579.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_scythe\_version.xsl](attachments/8193301/8127580.xsl)
-(application/octet-stream)  
-
-
+In order to test the Scythe (scythe/0.991) performance on Tusker, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Scythe on Tusker are shown in the table below:
+{{< readfile file="/static/html/scythe.html" >}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/sickle.md b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/sickle.md
index e2235b21..63d024da 100644
--- a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/sickle.md
+++ b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/sickle.md
@@ -1,249 +1,86 @@
-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.  [Pre-Processing Tools](Pre-Processing-Tools_8193298.html)
++++
+title = "Sickle"
+description =  "How to run Sickle on HCC resources"
+weight = "10"
++++
 
-<span id="title-text"> HCC-DOCS : Sickle </span>
-================================================
 
-Created by <span class="author"> Adam Caprez</span>, last modified by
-<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016
+[Sickle] (https://github.com/najoshi/sickle) is a windowed adaptive trimming tools for fastq files. Beside sliding window, Sickle uses quality and length thresholds to determine and trim low quality bases at both 3' end and 5' end of the reads.
 
-| Name   | Version | Resource |
-|--------|---------|----------|
-| sickle | 1.2     | Tusker   |
-
-|        |       |       |
-|--------|-------|-------|
-| sickle | 1.210 | Crane |
-
- 
-
-Sickle
-(<a href="https://github.com/najoshi/sickle" class="external-link">https://github.com/najoshi/sickle</a>)
-is a windowed adaptive trimming tools for fastq files. Beside sliding
-window, Sickle uses quality and length thresholds to determine and trim
-low quality bases at both 3' end and 5' end of the reads.
-
-Information about the Sickle command-line options can be shown by
-typing:
-
-**Additional Sickle Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.tusker ~]$ sickle --help
-```
+Information about the Sickle command-line options can be shown by typing:
+{{< highlight bash >}}
+$ sickle --help
+{{< /highlight >}}
 
 Sickle is single threaded program.
-
- 
-
-**Sickle for single-end reads**
+\\
+\\
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Sickle for single-end reads</span>
 
 The basic usage of Sickle for single-end reads is:
-
-**General Sickle Usage for Single-End Reads**
-
-``` syntaxhighlighter-pre
-sickle se -t [solexa|illumina|sanger] -f input_reads.fastq -o output_reads_trimmed.fastq
-```
-
-where **input\_reads.fastq** is the input file of sequencing data in
-fastq format, and **output\_reads\_trimmed.fastq** is the trimmed output
-file. Another required option in **sickle se** is the **-t** option that
-based on the input data, accepts one of the following quality
-values: **solexa**, **illumina**, **sanger.**
-
-Simple SLURM Sickle script for Illumina single-end reads input file
-**input\_reads.fastq** is shown below:
-
-**sickle\_single.submit**
-
-\#!/bin/sh  
-\#SBATCH --job-name=Sickle  
-\#SBATCH --nodes=1  
-\#SBATCH --ntasks-per-node=1  
-\#SBATCH --time=168:00:00  
-\#SBATCH --mem=30gb  
-\#SBATCH --output=Sickle\_single.%J.out  
-\#SBATCH --error=Sickle\_single.%J.err
-
- 
-
-|                        |
-|------------------------|
-| module load sickle/1.2 |
-
-sickle se -t illumina -f input\_reads.fastq -o
-output\_reads\_trimmed.fastq
-
- 
-
-**Sickle for paired-end reads**
+{{< highlight bash >}}
+$ sickle se -t [solexa|illumina|sanger] -f input_reads.fastq -o output_reads_trimmed.fastq
+{{< /highlight >}}
+where **input_reads.fastq** is the input file of sequencing data in fastq format, and **output_reads_trimmed.fastq** is the trimmed output file. Another required option in `sickle se` is the **-t** option that based on the input data, accepts one of the following quality values: **solexa**, **illumina**, **sanger**.
+\\
+\\
+\\
+Simple SLURM Sickle script for Illumina single-end reads input file `input_reads.fastq` is shown below:
+{{% panel header="`sickle_single.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=Sickle
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=Sickle_single.%J.out
+#SBATCH --error=Sickle_single.%J.err
+
+module load sickle/1.210
+
+sickle se -t illumina -f input_reads.fastq -o output_reads_trimmed.fastq
+{{< /highlight >}}
+{{% /panel %}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Sickle for paired-end reads</span>
 
 The basic usage of Sickle for paired-end reads is:
-
-**General Sickle Usage for Paired-End Reads**
-
-``` syntaxhighlighter-pre
-sickle pe -t [solexa|illumina|sanger] -f input_reads_pair_1.fastq -r input_reads_pair_2.fastq -o output_reads_trimmed_pair_1.fastq -p output_reads_trimmed_pair_2.fastq -s output_reads_trimmed_single.fastq
-```
-
-where **input\_reads\_pair\_1.fastq**
-and **input\_reads\_pair\_2.fastq** are the input fastq files of the
-sequencing data, and
-respectively, **output\_reads\_trimmed\_pair\_1.fastq**
-and **output\_reads\_trimmed\_pair\_2.fastq** are the trimmed output
-files. **Sickle pe** also
-prints **output\_reads\_trimmed\_single.fastq** file that contains reads
-that passed the filter in one pair, but not in the other read pair.
-Sickle supports three types of quality values: **solexa**, **illumina**,
-**sanger**, and this type must be specified using the **-t** option.
-
-Simple SLURM Sickle script for Sanger paired-end reads input
-files **input\_reads\_pair\_1.fastq**
-and ****input\_reads\_pair\_2.fastq**** is shown below:
-
-**sickle\_paired.submit**
-
-\#!/bin/sh  
-\#SBATCH --job-name=Sickle  
-\#SBATCH --nodes=1  
-\#SBATCH --ntasks-per-node=1  
-\#SBATCH --time=168:00:00  
-\#SBATCH --mem=30gb  
-\#SBATCH --output=Sickle\_paired.%J.out  
-\#SBATCH --error=Sickle\_paired.%J.err
-
- 
-
-|                        |
-|------------------------|
-| module load sickle/1.2 |
-
-sickle pe -t sanger -f input\_reads\_pair\_1.fastq -r
-input\_reads\_pair\_2.fastq -o output\_reads\_trimmed\_pair\_1.fastq -p
-output\_reads\_trimmed\_pair\_2.fastq -s
-output\_reads\_trimmed\_single.fastq
-
- 
-
-**Sickle Output**
-
-Sickle returns fastq file of reads with trimmed low quality bases from
-both 3' and 5' ends. Sickle reduces the sequence length, while the
-number of sequences in the output file stays the same.
-
- 
-
-**Useful Information**
-
-In order to test the SICKLE (sickle/1.2) performance on Tusker, we used
-three paired-end input fastq files: **small\_1.fastq**,
-**small\_2.fastq**, **medium\_1.fastq**, **medium\_2.fastq**,
-**large\_1.fastq**, **large\_2.fastq**. Some statistics about the input
-files and the time and memory resources required for SICKLE are shown on
-the table below:
-
- 
-
-**total \# of sequences**
-
-**total \# of bases**
-
-**total size in MB**
-
-**required time**
-
-**required memory**
-
-\# of used CPUs
-
-**small\_1.fastq**
-
-50,121
-
-2,506,050
-
-8.010 MB
-
-\~ 0.03 minutes
-
-\~ 0.05 GB
-
-1
-
-**small\_2.fastq**
-
-50,121
-
-2,506,050
-
-8.010 MB
-
-**medium\_1.fastq**
-
-786,742
-
-59,792,392
-
-152 MB
-
-\~ 0.2 minutes
-
-\~ 0.7 GB
-
-1
-
-**medium\_2.fastq**
-
-786,742
-
-59,792,392
-
-152 MB
-
-**large\_1.fastq**
-
-10,174,715
-
-1,027,646,215
-
-3,376 MB
-
-\~ 3 minutes
-
-\~ 13 GB
-
-1
-
-**large\_2.fastq**
-
-10,174,715
-
-1,027,646,215
-
-3,376 MB
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_sickle\_module.xsl](attachments/8193302/8127581.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193302/8127582.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_sickle\_version.xsl](attachments/8193302/8127583.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193302/8127584.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_sickle\_version.xsl](attachments/8193302/8127585.xsl)
-(application/octet-stream)  
-
-
+{{< highlight bash >}}
+$ sickle pe -t [solexa|illumina|sanger] -f input_reads_pair_1.fastq -r input_reads_pair_2.fastq -o output_reads_trimmed_pair_1.fastq -p output_reads_trimmed_pair_2.fastq -s output_reads_trimmed_single.fastq
+{{< /highlight >}}
+where **input_reads_pair_1.fastq** and **input_reads_pair_2.fastq** are the input fastq files of the sequencing data, and respectively, **output_reads_trimmed_pair_1.fastq** and **output_reads_trimmed_pair_2.fastq** are the trimmed output files. **sickle pe** also prints **output_reads_trimmed_single.fastq** file that contains reads that passed the filter in one pair, but not in the other read pair. Sickle supports three types of quality values: **solexa**, **illumina**, **sanger**, and this type must be specified using the **-t** option.
+\\
+\\
+\\
+Simple SLURM Sickle script for Sanger paired-end reads input files `input_reads_pair_1.fastq` and `input_reads_pair_2.fastq` is shown below:
+{{% panel header="`sickle_paired.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=Sickle
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=Sickle_paired.%J.out
+#SBATCH --error=Sickle_paired.%J.err
+
+module load sickle/1.210
+
+sickle pe -t sanger -f input_reads_pair_1.fastq -r input_reads_pair_2.fastq -o output_reads_trimmed_pair_1.fastq -p output_reads_trimmed_pair_2.fastq -s output_reads_trimmed_single.fastq
+{{< /highlight >}}
+{{% /panel %}}
+
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Sickle Output</span>
+
+Sickle returns fastq file of reads with trimmed low quality bases from both 3' and 5' ends. Sickle reduces the sequence length, while the number of sequences in the output file stays the same.
+\\
+\\
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Useful Information</span>
+
+In order to test the Sickle (sickle/1.210) performance on Tusker, we used three paired-end input fastq files, `small_1.fastq` and `small_2.fastq`, `medium_1.fastq` and `medium_2.fastq`, and `large_1.fastq` and `large_2.fastq`. Some statistics about the input files and the time and memory resources used by Sickle on Tusker are shown in the table below:
+{{< readfile file="/static/html/sickle.html" >}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/tagcleaner.md b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/tagcleaner.md
index 069adb96..b1c99142 100644
--- a/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/tagcleaner.md
+++ b/content/guides/running_applications/bioinformatics_tools/pre_processing_tools/tagcleaner.md
@@ -1,102 +1,47 @@
-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.  [Pre-Processing Tools](Pre-Processing-Tools_8193298.html)
++++
+title = "TagCleaner"
+description =  "How to run TagCleaner on HCC resources"
+weight = "10"
++++
 
-<span id="title-text"> HCC-DOCS : TagCleaner </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 |
-|------------|---------|----------|
-| tagcleaner | 0.16    | Crane    |
-
- 
-
-TagCleaner
-(<a href="http://tagcleaner.sourceforge.net/" class="external-link">http://tagcleaner.sourceforge.net/</a>)
-is a tool used to automatically detect and remove tag sequences from
-genomic and metagenomic sequence data. These additional tag sequences
-can contain deletions or insertions due to sequencing limitations.
+[TagCleaner] (http://tagcleaner.sourceforge.net/) is a tool used to automatically detect and remove tag sequences from genomic and metagenomic sequence data. These additional tag sequences can contain deletions or insertions due to sequencing limitations.
 
 The basic usage of TagCleaner is:
+{{< highlight bash >}}
+$ tagcleaner.pl [-fasta|-fastq] input_reads.[fasta|fastq] [-predict|-tag3|-tag5] [options]
+{{< /highlight >}}
+where **input_reads.[fasta|fastq]** is an input file of sequence data in fasta/fastq format, and **options** are additional parameters that can be found in the [TagCleaner
+manual] (http://tagcleaner.sourceforge.net/manual.html).
 
-**General TagCleaner Usage**
-
-``` syntaxhighlighter-pre
-tagcleaner.pl [-fasta|-fastq] input_reads.[fasta|fastq] [-predict|-tag3|-tag5] [options]
-```
-
-where **input\_reads.\[fasta\|fastq\]** is an input file of sequence
-data in fasta/fastq format, and **options** are additional parameters
-that can be found in the TagCleaner
-manual: <a href="http://tagcleaner.sourceforge.net/manual.html" class="external-link">http://tagcleaner.sourceforge.net/manual.html</a>.
-Required parameter for TagCleaner is the tag sequence. If the tag
-sequence is unknown, then the **-predict** option will provide the
-predicted tag sequence to the user. If the tag sequence is known and is
-found at the 3' end of the read, then the option **-tag3
-&lt;tag\_sequence&gt;** is used. If the tag sequence is known and is
-found at the 5' end of the read, the the option **-tag5
-&lt;tag\_sequence&gt;** is used.
+Required parameter for TagCleaner is the tag sequence. If the tag sequence is unknown, then the **-predict** option will provide the predicted tag sequence to the user. If the tag sequence is known and is found at the 3' end of the read, then the option **-tag3 &lt;tag_sequence&gt;** is used. If the tag sequence is known and is found at the 5' end of the read, the the option **-tag5 &lt;tag_sequence&gt;** is used.
 
 More information about the TagCleaner options can be found by using:
-
-**Additional TagCleaner Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.crane ~]$ tagcleaner.pl --help
-```
-
-Simple TagCleaner script for removing known 3' and 5' tag sequences
-(<span style="color: rgb(0,0,0);">NNNCCAAACACACCCAACACA
-and TGTGTTGGGTGTGTTTGGNNN respectively) is shown below:</span>
-
-**tagcleaner.submit**
-
-\#!/bin/sh  
-\#SBATCH --job-name=TagCleaner  
-\#SBATCH --nodes=1  
-\#SBATCH --ntasks-per-node=1  
-\#SBATCH --time=168:00:00  
-\#SBATCH --mem=20gb  
-\#SBATCH --output=TagCleaner.%J.out  
-\#SBATCH --error=TagCleaner.%J.err
-
- 
-
-|                             |
-|-----------------------------|
-| module load tagcleaner/0.16 |
-
-tagcleaner.pl -fasta input\_reads.fasta -tag3 NNNCCAAACACACCCAACACA
--tag5 TGTGTTGGGTGTGTTTGGNNN
-
-TagCleaner is single threaded program, and therefore both **\#SBATCH
---nodes** and** \#SBATCH --ntasks-per-node** are set to **1.**
-
-**  
-**
-
-**TagCleaner Output**
-
-TagCleaner returns fasta or fastq file of reads with removed tag
-sequences.
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_tagcleaner\_module.xsl](attachments/8193300/8127575.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193300/8127576.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_tagcleaner\_version.xsl](attachments/8193300/8127577.xsl)
-(application/octet-stream)  
-
-
+{{< highlight bash >}}
+$ tagcleaner.pl --help
+{{< /highlight >}}
+\\
+Simple TagCleaner script for removing known 3' and 5' tag sequences (`NNNCCAAACACACCCAACACA` and `TGTGTTGGGTGTGTTTGGNNN` respectively) is shown below:
+{{% panel header="`tagcleaner.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=TagCleaner
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=TagCleaner.%J.out
+#SBATCH --error=TagCleaner.%J.err
+
+module load tagcleaner/0.16
+
+tagcleaner.pl -fasta input_reads.fasta -tag3 NNNCCAAACACACCCAACACA -tag5 TGTGTTGGGTGTGTTTGGNNN
+{{< /highlight >}}
+{{% /panel %}}
+
+TagCleaner is single threaded program, 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;">TagCleaner Output</span>
+
+TagCleaner returns fasta or fastq file of reads with removed tag sequences.
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/qiime.md b/content/guides/running_applications/bioinformatics_tools/qiime.md
index b8ad2d3d..b9b818c2 100644
--- a/content/guides/running_applications/bioinformatics_tools/qiime.md
+++ b/content/guides/running_applications/bioinformatics_tools/qiime.md
@@ -44,6 +44,7 @@ Sample QIIME submit script to run **pick_open_reference_otus.py** is:
 #SBATCH --error=qiime.%J.err
 
 module load qiime/2.0
+
 pick_open_reference_otus.py --parallel --jobs_to_start $SLURM_CPUS_ON_NODE -i /work/[groupname]/[username]/input.fasta -o /work/[groupname]/[username]/project/out_${SLURM_JOB_ID}
 
 {{< /highlight >}}
diff --git a/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/_index.md b/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/_index.md
index b2f7d0af..8893f7f9 100644
--- a/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/_index.md
@@ -1,14 +1,7 @@
-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 : Reference-Based Assembly Tools </span>
-========================================================================
-
-Created by <span class="author"> Adam Caprez</span> on Sep 04, 2014
-
- 
-
++++
+title = "Reference-Based Assembly Tools"
+description = "How to use reference based assembly tools on HCC machines"
+weight = "52"
++++
 
+{{% children %}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/cufflinks.md b/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/cufflinks.md
index e34971cd..33d19a0f 100644
--- a/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/cufflinks.md
+++ b/content/guides/running_applications/bioinformatics_tools/reference_based_assembly_tools/cufflinks.md
@@ -1,2858 +1,83 @@
-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.  [Reference-Based Assembly
-    Tools](Reference-Based-Assembly-Tools_8193313.html)
-
-<span id="title-text"> HCC-DOCS : Cufflinks </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 |
-|-----------|---------|----------|
-| cufflinks | 2.0.2   | Tusker   |
-| cufflinks | 2.1.1   | Tusker   |
-| cufflinks | 2.2     | Tusker   |
-
-|           |     |       |
-|-----------|-----|-------|
-| cufflinks | 2.1 | Crane |
-| cufflinks | 2.2 | Crane |
-
- 
-
-Cufflinks
-(<a href="http://cufflinks.cbcb.umd.edu/" class="external-link">http://cufflinks.cbcb.umd.edu/</a>)
-is a transcript assembly program that includes a number of tools for
-analyzing RNA-Seq data. These tools assemble aligned RNA-Seq reads into
-transcripts, estimate their abundances, test for differential expression
-and regulation transcriptome-wide, and provide transcript
-quantification. Some of the tools part of Cufflinks can be run
-individually, while other are part of a larger workflow.
-
-The basic usage of Cufflinks is: 
-
-**General Cufflinks Usage**
-
-``` syntaxhighlighter-pre
-cufflinks [options] input_alignments.[sam|bam]
-```
-
-where **input\_alignments.\[sam\|bam\]** is sorted input file of RNA-Seq
-read alignments in SAM/BAM format. The RNA-Seq read mapper
-TopHat/TopHat2 produces output in this format and is recommended to be
-used with Cufflinks, although SAM/BAM alignments produced from any
-aligner are accepted. More advanced Cufflinks options can be found in
-the
-manual: <a href="http://cufflinks.cbcb.umd.edu/manual.html" class="external-link">http://cufflinks.cbcb.umd.edu/manual.html</a>,
-or by typing:
-
-**Additional Cufflinks Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.tusker ~]$ cufflinks -h
-```
-
-An example of how to run Cufflinks on Tusker with alignment file in SAM
-format, output directory *cufflinks\_output/* and 8 CPUs is shown below:
-
-**cufflinks.submit**
-
-\#!/bin/sh  
-\#SBATCH --job-name=Cufflinks  
-\#SBATCH --nodes=1  
-\#SBATCH --ntasks-per-node=8  
-\#SBATCH --time=168:00:00  
-\#SBATCH --mem=50gb  
-\#SBATCH --output=Cufflinks.%J.out  
-\#SBATCH --error=Cufflinks.%J.err
-
- 
-
-|                           |
-|---------------------------|
-| module load cufflinks/2.2 |
-
-cufflinks input\_alignments.sam -o cufflinks\_output/ -p
-$SLURM\_NTASKS\_PER\_NODE
-
- 
-
-The program **cufflinks** produces number of files in its predefined
-output directory *cufflinks\_output/*. Some of the generated files are:
-
--   **transcripts.gtf**: The GTF file contains Cufflinks' assembled
-    isoforms where there is one GTF record per row, and each record
-    represents either a transcript or an exon within a transcript
--   **isoforms.fpkm\_tracking**: This file contains the estimated
-    isoform-level expression values in the generic FPKM Tracking Format
--   **genes.fpkm\_tracking**: This file contains the estimated
-    gene-level expression values in the generic FPKM Tracking Format
-
- 
++++
+title = "Cufflinks"
+description =  "How to run Cufflinks on HCC resources"
+weight = "10"
++++
+
+
+[Cufflinks] (http://cole-trapnell-lab.github.io/cufflinks/) is a transcript assembly program that includes a number of tools for analyzing RNA-Seq data. These tools assemble aligned RNA-Seq reads into transcripts, estimate their abundances, test for differential expression and regulation, and provide transcript quantification. Some of the tools part of Cufflinks can be run individually, while others are part of a larger workflow.
+
+The basic usage of Cufflinks is:
+{{< highlight bash >}}
+$ cufflinks [options] input_alignments.[sam|bam]
+{{< /highlight >}}
+where `input_alignments.[sam|bam]` is sorted input file of RNA-Seq read alignments in SAM/BAM format. The RNA-Seq read mapper TopHat/TopHat2 produces output in this format and is recommended to be used with Cufflinks, although SAM/BAM alignments produced from any aligner are accepted. 
+
+More advanced Cufflinks options can be found in [the manual] (http://cole-trapnell-lab.github.io/cufflinks/manual/) or by typing:
+{{< highlight bash >}}
+$ cufflinks -h
+{{< /highlight >}}
+\\
+An example of how to run Cufflinks on Crane with alignment file in SAM format, output directory `cufflinks_output` and 8 CPUs is shown below:
+{{% panel header="`cufflinks.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=Cufflinks
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=Cufflinks.%J.out
+#SBATCH --error=Cufflinks.%J.err
+
+module load cufflinks/2.2
+
+cufflinks input_alignments.sam -o cufflinks_output/ -p ${SLURM_NTASKS_PER_NODE}
+{{< /highlight >}}
+{{% /panel %}}
+\\
+The program **cufflinks** produces number of files in its predefined output directory `cufflinks_output/`. Some of the generated files are:
+
+- **transcripts.gtf**: The GTF file contains Cufflinks' assembled isoforms where there is one GTF record per row, and each record represents either a transcript or an exon within a transcript
+- **isoforms.fpkm_tracking**: This file contains the estimated isoform-level expression values in the generic FPKM Tracking Format
+- **genes.fpkm_tracking**: This file contains the estimated gene-level expression values in the generic FPKM Tracking Format
+
+\\
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Available commands</span>
 
 Beside **cufflinks**, the Cufflinks package includes the following
 programs:
 
--   **Cuffcompare  
-    **
-
-Cuffcompare uses the Cufflinks' GTF output as an input file and compares
-the assembled transcripts to a reference annotation. An example of
-comparing the already annotated genome **known\_annotation.gtf** with
-the new annotation **new\_annotation.gtf** follows:
-
-**General Cuffcompare Usage**
-
-``` syntaxhighlighter-pre
-cuffcompare -r known_annotation.gtf new_annotation.gtf
-```
-
-This tool reports various statistics about the transcripts, as well as a
-GTF file containing all transfrags in each sample.
-
--   **Cuffmerge**
-
-This program allows merging of multiple Cufflinks GTF files. An example
-of merging multiple GTF files with full paths defined in the file
-**list\_GTF.txt** and 8 CPUs is shown below:**  
-**
-
-**General Cuffmerge Usage**
+- **Cuffcompare**
 
-``` syntaxhighlighter-pre
-cuffmerge list_GTF.txt -p 8
-```
+**cuffcompare** uses the Cufflinks' GTF output as an input file and compares the assembled transcripts to a reference annotation. 
 
-The cuffmerge output is single unified transcript file.
+Example of comparing the already annotated genome `known_annotation.gtf` with the new annotation `new_annotation.gtf`:
+{{< highlight bash >}}
+$ cuffcompare -r known_annotation.gtf new_annotation.gtf
+{{< /highlight >}}
 
--   **Cuffdiff**
+This tool reports various statistics about the transcripts, as well as a GTF file containing all transfrags in each sample.
 
-Cuffdiff is used to identify differentially expressed transcripts. An
-example of **cuffdiff** for the annotated transcripts for the new
-genome, **new\_annotations.gtf,** with 3 SAM alignment files generated
-from TopHat and 8 CPUs follows:
+-  **Cuffmerge**
 
-**General Cuffdiff Usage**
+This program allows merging of multiple Cufflinks GTF files.
 
-``` syntaxhighlighter-pre
-cuffdiff new_alignments.gtf sample_1.sam, sample_2.sam, sample_3.sam -p 8
-```
+Example of merging multiple GTF files with full paths defined in the file `list_GTF.txt` and 8 CPUs is:
+{{< highlight bash >}}
+$ cuffmerge list_GTF.txt -p 8
+{{< /highlight >}}
 
-Cuffdiff prints multiple output files, such as: *FPKM tracking files*,
-*count tracking files*, *read group tracking files*, *differential
-expression tests*, *differential splicing tests*, *differential coding
-output*, *differential promoter use*, *read group info*, and *run info.*
+The output of **cuffmerge** is single unified transcript file.
 
-Attachments:
-------------
+- **Cuffdiff**
 
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_cufflinks\_module.xsl](attachments/8193314/8127612.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_cufflinks\_version.xsl](attachments/8193314/8127613.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_cufflinks\_version.xsl](attachments/8193314/8127615.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/9863876.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/9863854.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/9863915.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/9863937.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/10387516.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/10387477.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/11632695.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/10944565.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/10944605.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11632803.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/11632764.xml)
-(application/octet-stream)  
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-[crane\_modules.xml](attachments/8193314/11632827.xml)
-(application/octet-stream)  
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-[tusker\_modules.xml](attachments/8193314/11632891.xml)
-(application/octet-stream)  
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-[crane\_modules.xml](attachments/8193314/11632852.xml)
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-[crane\_modules.xml](attachments/8193314/11632965.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11632941.xml)
-(application/octet-stream)  
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-[tusker\_modules.xml](attachments/8193314/11633016.xml)
-(application/octet-stream)  
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-[crane\_modules.xml](attachments/8193314/11633044.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11633093.xml)
-(application/octet-stream)  
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-[crane\_modules.xml](attachments/8193314/11633119.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11633163.xml)
-(application/octet-stream)  
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-[crane\_modules.xml](attachments/8193314/11633187.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11633242.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/11633317.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11633293.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11633383.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/11633342.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/11633407.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11633446.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/11633515.xml)
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-[tusker\_modules.xml](attachments/8193314/11633486.xml)
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-[tusker\_modules.xml](attachments/8193314/11633560.xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/11633586.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11633645.xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/11633797.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11633686.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11633733.xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11633773.xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11633876.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/11633826.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/11634231.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11633940.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11633980.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11634028.xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11634070.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11634110.xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11634159.xml)
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-[tusker\_modules.xml](attachments/8193314/11634207.xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/11634301.xml)
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-[crane\_modules.xml](attachments/8193314/11634262.xml)
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-[crane\_modules.xml](attachments/8193314/11634325.xml)
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-[tusker\_modules.xml](attachments/8193314/11634435.xml)
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-(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" />
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/30447671.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
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-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/30447836.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/30448006.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/30447913.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/30447971.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/30448071.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/30448106.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/30448420.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/30448312.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/30448456.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/30448550.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/30448683.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/30448596.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/30448647.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" />
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/30448857.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/30448893.xml)
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-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/30448965.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/30449001.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/33685549.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/33685622.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/33685660.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/33685733.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/33685772.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/33685845.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/33685877.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/33685950.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/33686014.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/33686087.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/33686118.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/33686191.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/33686257.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/33686330.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/33687793.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/33687866.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/33688397.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/33688476.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/33689726.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/33689799.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/33689946.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/33690019.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/35323996.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/35324059.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/35324106.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/35324169.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/35324444.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/35324639.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/35324574.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/35324864.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/35324929.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/35325029.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/35325661.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/35325198.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/35325241.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/35325284.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/35325591.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/35325708.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/35325774.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/35326169.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/35326761.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/35326695.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193314/9863802.xml)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[tusker\_modules.xml](attachments/8193314/9863803.xml)
-(application/octet-stream)  
+**cuffdiff** is used to identify differentially expressed transcripts. 
 
+Example of **cuffdiff** for the annotated transcripts for the new genome, `new_annotations.gtf`, with 3 SAM alignment files generated from TopHat and 8 CPUs:
+{{< highlight bash >}}
+$ cuffdiff new_alignments.gtf sample_1.sam, sample_2.sam, sample_3.sam -p 8
+{{< /highlight >}}
 
+**cuffdiff** prints multiple output files, such as `FPKM tracking files`, `count tracking files`, `read group tracking files`, `differential expression tests`, `differential splicing tests`, `differential coding output`, `differential promoter use`, `read group info`, and `run info`.
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/_index.md b/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/_index.md
index 6eaccb60..243f1b5b 100644
--- a/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/_index.md
@@ -1,14 +1,7 @@
-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 : Tools for Removing/Detecting Redundant Sequences </span>
-==========================================================================================
-
-Created by <span class="author"> Adam Caprez</span> on Sep 04, 2014
-
- 
-
++++
+title = "Tools for Removing/Detecting Redundant Sequences"
+description = "How to use tools for removing/detecting redundant sequences on HCC machines"
+weight = "52"
++++
 
+{{% children %}}
diff --git a/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cap3.md b/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cap3.md
index 8737f3be..3e215c32 100644
--- a/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cap3.md
+++ b/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cap3.md
@@ -1,158 +1,53 @@
-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.  [Tools for Removing/Detecting Redundant Sequences](8193310.html)
++++
+title = "CAP3"
+description =  "How to run CAP3 on HCC resources"
+weight = "10"
++++
 
-<span id="title-text"> HCC-DOCS : CAP3 </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 |
-|------|---------|----------|
-| cap3 | 122107  | Crane    |
-
- 
-
-CAP3 (Contig Assembly Program) is a DNA sequence assembly program for
-small-scale assembly with or without quality values.
+CAP3 (Contig Assembly Program) is a DNA sequence assembly program for small-scale assembly with or without quality values.
 
 The basic usage of CAP3 is:
-
-**General CAP3 Usage**
-
-``` syntaxhighlighter-pre
-cap3 input_reads.fasta [options] > output.txt
-```
-
-where **input\_reads.fasta** is an input file of sequence reads in fasta
-format, and **options** are optional parameters that can be found in the
-CAP3
-manual: <a href="http://computing.bio.cam.ac.uk/local/doc/cap3.txt" class="external-link">http://computing.bio.cam.ac.uk/local/doc/cap3.txt</a>.
-
-More information about the CAP3 program can be shown my typing:
-
-**Additional CAP3 Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.crane ~]$ cap3
-```
-
-on the command line.
-
+{{< highlight bash >}}
+$ cap3 input_reads.fasta [options] > output.txt
+{{< /highlight >}}
+where `input_reads.fasta` is an input file of sequence reads in fasta format, and `options` are optional parameters that can be found by typing:
+{{< highlight bash >}}
+$ cap3
+{{< /highlight >}}
+\\
 An example of how to run basic CAP3 SLURM script on Crane is shown
 below:
-
-**cap3.submit**
-
-\#!/bin/sh  
-\#SBATCH --job-name=CAP3  
-\#SBATCH --nodes=1  
-\#SBATCH --ntasks-per-node=1  
-\#SBATCH --time=168:00:00  
-\#SBATCH --mem=20gb  
-\#SBATCH --output=CAP3.%J.out  
-\#SBATCH --error=CAP3.%J.err
-
- 
-
-|                         |
-|-------------------------|
-| module load cap3/122107 |
-
-cap3 input\_reads.fasta &gt; output.txt
-
-CAP3 is single threaded program, and therefore both **\#SBATCH --nodes**
-and **\#SBATCH --ntasks-per-node** are set to **1**.
-
- 
-
-**CAP3 Output**
-
-CAP3 returns few output files:
-*input\_reads.fasta.cap.singlets*, *input\_reads.fasta.cap.contigs**,*** *input\_reads.fasta.cap.contigs.links*, *input\_reads.fasta.cap.qual*, *input\_reads.fasta.cap.ace*, *input\_reads.fasta.cap.info*.
-
-The consensus fasta sequences are saved in the
-file ***input\_reads.fasta.cap.contigs***, while the reads that are not
-used in the assembly are stored in the fasta
-file ***input\_reads.fasta.cap.singlets***.
-
- 
-
-**Useful Information**
-
-In order to test the CAP3 (cap3/122107) performance on Crane, we grouped
-separately three nucleotide datasets, **small.fasta**, **medium.fasta**
-and **large.fasta**. Some statistics about the input datasets and the
-time and memory resources required for CAP3 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>total # of bases</strong></p></th>
-<th><p><strong>total size in MB</strong></p></th>
-<th><p><strong>required time</strong></p></th>
-<th><p><strong>required memory</strong></p></th>
-<th># of used CPUs</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><p><strong>small.fasta</strong></p></td>
-<td><p>41,715</p></td>
-<td><p>35,581,740</p></td>
-<td><p>37.627 MB</p></td>
-<td><p>~ 1.6 hours</p></td>
-<td><p>~ 1.5 GB</p></td>
-<td>1</td>
-</tr>
-<tr class="even">
-<td><p><strong>medium.fasta</strong></p></td>
-<td><p>110,478</p></td>
-<td><p>147,543,113</p></td>
-<td><p>149 MB</p></td>
-<td><p>~ 2 hours</p></td>
-<td><p>~ 5 GB</p></td>
-<td>1</td>
-</tr>
-<tr class="odd">
-<td><p><strong>large.fasta</strong></p></td>
-<td><p>592,593</p></td>
-<td><p>827,629,204</p></td>
-<td><p>836 MB</p></td>
-<td><p>~ 12 hours</p></td>
-<td><p>~ 28 GB</p></td>
-<td>1</td>
-</tr>
-</tbody>
-</table>
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_cap3\_module.xsl](attachments/8193311/8127606.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_cap3\_version.xsl](attachments/8193311/8127607.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193311/8127608.xml)
-(application/octet-stream)  
-
-
+{{% panel header="`cap3.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=CAP3
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=CAP3.%J.out
+#SBATCH --error=CAP3.%J.err
+
+module load cap3/122107
+
+cap3 input_reads.fasta > output.txt
+{{< /highlight >}}
+{{% /panel %}}
+
+CAP3 is single threaded program, 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;">CAP3 Output</span>
+
+CAP3 returns few output files, `input_reads.fasta.cap.singlets`, `input_reads.fasta.cap.contigs`, `input_reads.fasta.cap.contigs.links`, `input_reads.fasta.cap.qual`, `input_reads.fasta.cap.ace`, `input_reads.fasta.cap.info`.
+
+The consensus fasta sequences are saved in the file `input_reads.fasta.cap.contigs`, while the reads that are not used in the assembly are stored in the fasta file `input_reads.fasta.cap.singlets`.
+\\
+\\
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">Useful Information</span>
+
+In order to test the CAP3 (cap3/122107) performance on Crane, we created separately three nucleotide datasets, `small.fasta`, `medium.fasta` and `large.fasta`. Some statistics about the input datasets and the time and memory resources used by CAP3 on Crane are shown in the table below:
+{{< readfile file="/static/html/cap3.html" >}}
\ No newline at end of file
diff --git a/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cd_hit.md b/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cd_hit.md
index 3d35a767..73e0b185 100644
--- a/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cd_hit.md
+++ b/content/guides/running_applications/bioinformatics_tools/removing_detecting_redundant_sequences/cd_hit.md
@@ -1,116 +1,58 @@
-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.  [Tools for Removing/Detecting Redundant Sequences](8193310.html)
-
-<span id="title-text"> HCC-DOCS : CD-HIT </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 |
-|--------|---------|----------|
-| cd-hit | 4.6     | Crane    |
-
++++
+title = "CD-HIT"
+description =  "How to run CD-HIT on HCC resources"
+weight = "10"
++++
  
 
-CD-HIT (Cluster Database at High Identity with Tolerance)
-(<a href="http://weizhong-lab.ucsd.edu/cd-hit/" class="external-link">http://weizhong-lab.ucsd.edu/cd-hit/</a>) is
-a program for clustering and comparing nucleotide or protein sequences.
-CD-HIT is very fast and can handle large DNA/RNA datasets.
+CD-HIT (Cluster Database at High Identity with Tolerance), http://weizhong-lab.ucsd.edu/cd-hit, is a program for clustering and comparing nucleotide or protein sequences. CD-HIT is very fast and can handle large DNA/RNA datasets.
 
-Some of the most frequently used executables from the CD-HIT package
-are: CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454,
-CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU, CD-HIT-LAP and CD-HIT-DUP:
+Some of the most frequently used executables from the CD-HIT package are: CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU, CD-HIT-LAP and CD-HIT-DUP:
 
--   <span style="line-height: 1.4285715;">CD-HIT or CD-HIT-EST clusters
-    similar proteins or DNAs into clusters that meet a defined
-    similarity threshold</span>
--   <span style="line-height: 1.4285715;">CD-HIT-2D (CD-HIT-EST-2D)
-    compares 2 datasets and identifies the sequences in db2 that are
-    similar to db1 above a given threshold</span>
--   <span style="line-height: 1.4285715;">CD-HIT-454 identifies natural
-    and artificial duplicates from pyrosequencing reads</span>
--   <span style="line-height: 1.4285715;">CD-HIT-OTU clusters rRNA tags
-    into OTUs</span>
--   <span style="line-height: 1.4285715;">CD-HIT-DUP identifies
-    duplicates from single or paired Illumina reads</span>
--   <span style="line-height: 1.4285715;">CD-HIT-LAP identifies
-    overlapping reads</span>
-
-<span style="line-height: 1.4285715;">Detailed overview of the whole
-CD-HIT package and executables can be found in the CD-HIT user's
-guide: <a href="http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit_user_guide" class="external-link">http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit_user_guide</a>.</span>
+- CD-HIT or CD-HIT-EST clusters similar proteins or DNAs into clusters that meet a defined similarity threshold
+- CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a given threshold
+- CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads
+- CD-HIT-OTU clusters rRNA tags into OTUs
+- CD-HIT-DUP identifies duplicates from single or paired Illumina reads
+- CD-HIT-LAP identifies overlapping reads
 
+Detailed overview of the whole CD-HIT package and executables can be found in the 
+[CD-HIT user's guide] (http://weizhongli-lab.org/lab-wiki/doku.php?id=cd-hit-user-guide).
+\\
+\\
+\\
 The basic usage of CD-HIT is:
-
-**General CD-HIT Usage**
-
-``` syntaxhighlighter-pre
-cd-hit -i input_reads.fasta -o output [options]
-```
-
-where **input\_reads.fasta** is an input file of sequence reads in fasta
-format, **output** is the prefix of the output files,
-and **options** are optional parameters that can be found by typing:
-
-**Additional CD-HIT Options**
-
-``` syntaxhighlighter-pre
-[<username>@login.crane ~]$ cd-hit
-```
-
-<span style="line-height: 1.4285715;">CD-HIT is multi-threaded program,
-and therefore, using multiple threads is recommended. Thus, by setting
-the CD-HIT parameter **-T 0**, all CPUs defined in the SLURM script will
-be used. Setting the parameter **-M 0** allows unlimited usage of the
-available memory.</span>
-
+{{< highlight bash >}}
+$ cd-hit -i input_reads.fasta -o output [options]
+{{< /highlight >}}
+where `input_reads.fasta` is an input file of sequence reads in fasta format, `output` is the prefix of the output files, and `options` are optional parameters that can be found by typing:
+{{< highlight bash >}}
+$ cd-hit
+{{< /highlight >}}
+
+CD-HIT is multi-threaded program, and therefore, using multiple threads is recommended. By setting the CD-HIT parameter `-T 0`, all CPUs defined in the SLURM script will be used. Setting the parameter `-M 0` allows unlimited usage of the available memory.
+\\
+\\
+\\
 Simple SLURM CD-HIT script for Crane with 8 CPUs is given in addition:
-
-**cd-hit.submit**
-
-\#!/bin/sh  
-\#SBATCH --job-name=CD-HIT  
-\#SBATCH --nodes=1  
-\#SBATCH --ntasks-per-node=8  
-\#SBATCH --time=168:00:00  
-\#SBATCH --mem=50gb  
-\#SBATCH --output=CD-HIT.%J.out  
-\#SBATCH --error=CD-HIT.%J.err
-
- 
-
-|                        |
-|------------------------|
-| module load cd-hit/4.6 |
-
-cd-hit -i input\_reads.fasta -o output -M 0 -T 0
-
- 
-
-**CD-HIT Output**
-
-CD-HIT prints 2 files: *output* and *output.clstr*.
-
-***Output*** contains the final clustered non-redundant sequences in
-fasta format, while ***output.clstr*** has an information about the
-clusters with associated sequences.
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[cb\_cdhit\_module.xsl](attachments/8193312/8127609.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_cdhit\_version.xsl](attachments/8193312/8127610.xsl)
-(application/octet-stream)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[crane\_modules.xml](attachments/8193312/8127611.xml)
-(application/octet-stream)  
-
-
+{{% panel header="`cd-hit.submit`"%}}
+{{< highlight bash >}}
+#!/bin/sh
+#SBATCH --job-name=CD-HIT
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+#SBATCH --time=168:00:00
+#SBATCH --mem=10gb
+#SBATCH --output=CD-HIT.%J.out
+#SBATCH --error=CD-HIT.%J.err
+
+module load cd-hit/4.6
+
+cd-hit -i input_reads.fasta -o output -M 0 -T 0
+{{< /highlight >}}
+{{% /panel %}}
+\\
+\\
+<span style="color: rgb(0,0,0);font-size: 20.0px;line-height: 1.5;">CD-HIT Output</span>
+
+CD-HIT prints out 2 files: `output` and `output.clstr`. **`output`** contains the final clustered non-redundant sequences in fasta format, while **`output.clstr`** has an information about the clusters with its associated sequences.
\ No newline at end of file
diff --git a/static/html/cap3.html b/static/html/cap3.html
new file mode 100644
index 00000000..ef0c034f
--- /dev/null
+++ b/static/html/cap3.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">~ 1.6 hours</td>
+  <td colspan="1">~ 1.5 GB</td>
+  <td colspan="1">1</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">~ 2 hours</td>
+  <td colspan="1">~ 5 GB</td>
+  <td colspan="1">1</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">~ 12 hours</td>
+  <td colspan="1">~ 28 GB</td>
+  <td colspan="1">1</td>
+ </tr>
+ </tbody>
+ </table>
diff --git a/static/html/scythe.html b/static/html/scythe.html
new file mode 100644
index 00000000..1179b790
--- /dev/null
+++ b/static/html/scythe.html
@@ -0,0 +1,77 @@
+ <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_1.fastq</strong></td>
+  <td colspan="1">50,121</td>
+  <td colspan="1">2,506,050</td>
+  <td colspan="1">8.010</td>
+  <td colspan="1">~ 0.04 minutes</td>
+  <td colspan="1">~ 0.014 GB</td>
+  <td colspan="1">1</td>
+ </tr>
+ <tr>
+  <td colspan="1"><strong>small_2.fastq</strong></td>
+  <td colspan="1">50,121</td>
+  <td colspan="1">2,506,050</td>
+  <td colspan="1">8.010</td>
+  <td colspan="1">~ 0.04 minutes</td>
+  <td colspan="1">~ 0.014 GB</td>
+  <td colspan="1">1</td>
+ </tr>
+ <tr>
+  <td colspan="1"><strong>medium_1.fastq</strong></td>
+  <td colspan="1">786,742</td>
+  <td colspan="1">59,792,392</td>
+  <td colspan="1">152</td>
+  <td colspan="1">~ 1 minute</td>
+  <td colspan="1">~ 0.2 GB</td>
+  <td colspan="1">1</td>
+ </tr>
+ <tr>
+  <td colspan="1"><strong>medium_2.fastq</strong></td>
+  <td colspan="1">786,742</td>
+  <td colspan="1">59,792,392</td>
+  <td colspan="1">152</td>
+  <td colspan="1">~ 1 minute</td>
+  <td colspan="1">~ 0.2 GB</td>
+  <td colspan="1">1</td>
+ </tr>
+ <tr>
+  <td colspan="1"><strong>large_1.fastq</strong></td>
+  <td colspan="1">10,174,715</td>
+  <td colspan="1">1,027,646,215</td>
+  <td colspan="1">3,376</td>
+  <td colspan="1">~ 13 minutes</td>
+  <td colspan="1">~ 3 GB</td>
+  <td colspan="1">1</td>
+ </tr>
+ <tr>
+  <td colspan="1"><strong>large_2.fastq</strong></td>
+  <td colspan="1">10,174,715</td>
+  <td colspan="1">1,027,646,215</td>
+  <td colspan="1">3,376</td>
+  <td colspan="1">~ 17 minutes</td>
+  <td colspan="1">~ 6.5 GB</td>
+  <td colspan="1">1</td>
+ </tr>
+ </tbody>
+ </table>
\ No newline at end of file
diff --git a/static/html/sickle.html b/static/html/sickle.html
new file mode 100644
index 00000000..de522963
--- /dev/null
+++ b/static/html/sickle.html
@@ -0,0 +1,68 @@
+ <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_1.fastq</strong></td>
+  <td colspan="1">50,121</td>
+  <td colspan="1">2,506,050</td>
+  <td colspan="1">8.010</td>
+  <td colspan="1" rowspan="2">~ 0.03 minutes</td>
+  <td colspan="1" rowspan="2">~ 0.05 GB</td>
+  <td colspan="1" rowspan="2">1</td>
+ </tr>
+ <tr>
+  <td colspan="1"><strong>small_2.fastq</strong></td>
+  <td colspan="1">50,121</td>
+  <td colspan="1">2,506,050</td>
+  <td colspan="1">8.010</td>
+ </tr>
+ <tr>
+  <td colspan="1"><strong>medium_1.fastq</strong></td>
+  <td colspan="1">786,742</td>
+  <td colspan="1">59,792,392</td>
+  <td colspan="1">152</td>
+  <td colspan="1" rowspan="2">~ 0.2 minutes</td>
+  <td colspan="1" rowspan="2">~ 0.7 GB</td>
+  <td colspan="1" rowspan="2">1</td>
+ </tr>
+ <tr>
+  <td colspan="1"><strong>medium_2.fastq</strong></td>
+  <td colspan="1">786,742</td>
+  <td colspan="1">59,792,392</td>
+  <td colspan="1">152</td>
+ </tr>
+ <tr>
+  <td colspan="1"><strong>large_1.fastq</strong></td>
+  <td colspan="1">10,174,715</td>
+  <td colspan="1">1,027,646,215</td>
+  <td colspan="1">3,376</td>
+  <td colspan="1" rowspan="2">~ 3 minutes</td>
+  <td colspan="1" rowspan="2">~ 13 GB</td>
+  <td colspan="1" rowspan="2">1</td>
+ </tr>
+ <tr>
+  <td colspan="1"><strong>large_2.fastq</strong></td>
+  <td colspan="1">10,174,715</td>
+  <td colspan="1">1,027,646,215</td>
+  <td colspan="1">3,376</td>
+ </tr>
+ </tbody>
+ </table>
\ No newline at end of file
-- 
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