ILRI Research Computing

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====== seroba ======
SeroBA is a k-mer based Pipeline to identify the Serotype from Illumina NGS reads for given references. You can use SeroBA to download references from [[https://github.com/phe-bioinformatics/PneumoCaT|PneumoCaT]] to do identify the capsular type of Streptococcus pneumoniae.

===== Information =====

  * Version: 1.0.0
  * Added: November, 2018
  * Link: https://github.com/sanger-pathogens/seroba

===== Usage =====

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

Load one version into your environment and run it:
<code>$ module load seroba/1.0.0
$ seroba</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ sudo mkdir -p /export/apps/seroba/1.0.0
$ sudo chown aorth /export/apps/seroba/1.0.0
$ python3.6m -m venv /export/apps/seroba/1.0.0
$ source /export/apps/seroba/1.0.0/bin/activate
$ module load MUMer/3.23
$ pip3 install ariba pymummer biopython pyyaml
$ pip3 install seroba
$ sudo chown -R root:root /export/apps/seroba</code>