diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
index a709aaefa93ba8595ada3a63a2fdd789a7fb6081..deb9548ce639c06043447c45cc82884cdff53932 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
@@ -7,7 +7,7 @@ weight = "52"
[BLAST] (https://blast.ncbi.nlm.nih.gov/Blast.cgi) is a local alignment tool that finds similarity between sequences. This tool compares nucleotide or protein sequences to sequence databases, and calculates significance of matches. Sometimes these input sequences are large and using the command-line BLAST is required.
-The following pages, [Create Local BLAST Database](create_local_blast_database) and [Running BLAST Alignment](running_blast_alignment) describe how to run some of the most common BLAST executables as a single job using the SLURM scheduler on HCC.
+The following pages, [Create Local BLAST Database]({{<relref "create_local_blast_database" >}}) and [Running BLAST Alignment]({{<relref "running_blast_alignment" >}}) describe how to run some of the most common BLAST executables as a single job using the SLURM scheduler on HCC.
### Useful Information
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
index 6423e3f0457bd60c536cafabf8d7bf0d4a9868f2..babb649362326e24e93e20d7a42a70545a34b837 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
@@ -28,7 +28,7 @@ $ blastn -help
These BLAST alignment commands are multi-threaded, and therefore using the BLAST option **-num_threads <number_of_CPUs>** is recommended.
-HCC hosts multiple BLAST databases and indices on both Tusker and Crane. In order to use these resources, the ["biodata" module] (../../../biodata_module) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:
+HCC hosts multiple BLAST databases and indices on both Tusker and Crane. In order to use these resources, the ["biodata" module] ({{<relref "/guides/running_applications/bioinformatics_tools/biodata_module">}}) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:
- **16SMicrobial**
- **env_nt**
@@ -50,12 +50,13 @@ HCC hosts multiple BLAST databases and indices on both Tusker and Crane. In orde
- **tsa_nr**
- **tsa_nt**
-If you want to create and use a BLAST database that is not mentioned above, check [Create Local BLAST Database](create_local_blast_database).
+If you want to create and use a BLAST database that is not mentioned above, check [Create Local BLAST Database]({{<relref "create_local_blast_database" >}}).
Basic SLURM example of nucleotide BLAST run against the non-redundant **nt** BLAST database with `8 CPUs` is provided below. When running BLAST alignment, it is recommended to first copy the query and database files to the **/scratch/** directory of the worker node. Moreover, the BLAST output is also saved in this directory (**/scratch/blastn_output.alignments**). After BLAST finishes, the output file is copied from the worker node to your current work directory.
{{% notice info %}}
**Please note that the worker nodes can not write to the */home/* directories and therefore you need to run your job from your */work/* directory.**
+**This example will first copy your database to faster local storage called “scratch”. This can greatly improve performance!**
{{% /notice %}}
{{% panel header="`blastn_alignment.submit`"%}}
@@ -95,6 +96,7 @@ The default BLAST output is in pairwise format. However, BLAST’s parameter **-
Basic SLURM example of protein BLAST run against the non-redundant **nr **BLAST database with tabular output format and `8 CPUs` is shown below. Similarly as before, the query and database files are copied to the **/scratch/** directory. The BLAST output is also saved in this directory (**/scratch/blastx_output.alignments**). After BLAST finishes, the output file is copied from the worker node to your current work directory.
{{% notice info %}}
**Please note that the worker nodes can not write to the */home/* directories and therefore you need to run your job from your */work/* directory.**
+**This example will first copy your database to faster local storage called “scratch”. This can greatly improve performance!**
{{% /notice %}}
{{% panel header="`blastx_alignment.submit`"%}}
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
index 5d1e35101b995a53deeb2535ce4c70be5d6132f3..5b770061ec93f6a78c6ec0a37dfd86ea2306fa08 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
@@ -36,4 +36,4 @@ $ bwa COMMAND
or check the [BWA manual] (http://bio-bwa.sourceforge.net/bwa.shtml).
-The page[Running BWA Commands](running_bwa_commands) shows how to run BWA on HCC.
+The page [Running BWA Commands]({{<relref "running_bwa_commands" >}}) shows how to run BWA on HCC.
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
index 92a3208a05dd307f6d6ffeea5a0f43d595db117f..69ac4d03eb4609a8d6f06f160c461c874c874255 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
@@ -14,7 +14,7 @@ The basic usage of TopHat2 is:
{{< highlight bash >}}
$ [tophat|tophat2] [options] index_prefix [input_reads_pair_1.[fasta|fastq] input_reads_pair_2.[fasta|fastq] | input_reads.[fasta|fastq]]
{{< /highlight >}}
-where **index_prefix** is the basename of the genome index to be searched. This index is generated prior running TopHat/TopHat2 by using [Bowtie](bowtie)/[Bowtie2](bowtie2).
+where **index_prefix** is the basename of the genome index to be searched. This index is generated prior running TopHat/TopHat2 by using [Bowtie]({{<relref "bowtie" >}})/[Bowtie2]({{<relref "bowtie2" >}}).
TopHat2 uses single or comma-separated list of paired-end and single-end reads in fasta or fastq format. The single-end reads need to be provided after the paired-end reads.
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 7fd7db27144779be73422683ce4b5600295eaf5d..45f9d16e54f721e0f36814ae66aa650a57fdf13b 100644
--- a/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
@@ -80,4 +80,4 @@ 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)
+[Organisms]({{<relref "organisms" >}})
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
index 9399d8e3898979f4917535e1958c921605cc5717..efe441b273cf60f9e5580cbf00438943871e34c3 100644
--- a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
@@ -36,4 +36,4 @@ $ bamtools help COMMAND
or check the BamTools web, https://github.com/pezmaster31/bamtools/wiki.
-The page [Running BamTools Commands](running_bamtools_commands) shows how to run BamTools on HCC.
+The page [Running BamTools Commands]({{<relref "running_bamtools_commands" >}}) shows how to run BamTools on HCC.
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
index 0246ba99e4fbd988b0273676ef7983d0e8908aa4..df9a00e249745424df56d468de309da6f4971c81 100644
--- a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
@@ -42,4 +42,4 @@ $ samtools COMMAND
or check the [SAMtools manual] (http://www.htslib.org/doc/samtools.html).
-The page [Running SAMtools Commands](running_samtools_commands) shows how to run SAMtools on HCC.
+The page [Running SAMtools Commands]({{<relref "running_samtools_commands" >}}) shows how to run SAMtools on HCC.