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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.



See which versions are available:

$ module avail srst2

Load one version into your environment and run it:

$ module load srst2/git-73f885f5
$ srst2 --version

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.


Notes from the sysadmin during installation:

$ 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+
$ sudo chown -R root:root /export/apps/srst2/git-73f885f5

See also, the bioconda recipe for srst2.

srst2-software.txt · Last modified: 2023/08/10 07:43 by aorth