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 PneumoCaT to do identify the capsular type of Streptococcus pneumoniae.

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

See versions which are available:

$ module avail seroba

Load one version into your environment and run it:

$ module load seroba/1.0.0
$ seroba

Notes from the sysadmin during installation:

$ 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