ILRI Research Computing

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====== srst2 ======

This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.

===== Information =====

  * Version: git-73f885f5
  * Added: August, 2023
  * Link: https://github.com/katholt/srst2

===== Usage =====

See which versions are available:
<code>$ module avail srst2</code>

Load one version into your environment and run it:
<code>$ module load srst2/git-73f885f5
$ srst2 --version</code>

**Note:** Please use the %%''--threads''%% option to tell panaroo how many CPU cores/threads it should use. This number should match the number of CPUs you requested in your SLURM batch allocation.

===== Installation ======

Notes from the sysadmin during installation:

<code>$ module load python/2.7
$ sudo mkdir -p /export/apps/srst2/git-73f885f5
$ sudo chown aorth:aorth /export/apps/srst2/git-73f885f5
$ virtualenv /export/apps/srst2/git-73f885f5/venv
$ source /export/apps/srst2/git-73f885f5/venv/bin/activate
$ pip install scipy
$ pip install git+https://github.com/katholt/srst2
$ sudo chown -R root:root /export/apps/srst2/git-73f885f5</code>

See also, the [[https://github.com/bioconda/bioconda-recipes/blob/master/recipes/srst2/meta.yaml|bioconda recipe for srst2]].