Srst2

Introduction

Srst2 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. For more information, please check: Docker hub: https://hub.docker.com/r/staphb/srst2 Home page: https://github.com/katholt/srst2

Versions

  • 0.2.0

Commands

  • getmlst.py

  • srst2

  • slurm_srst2.py

Module

You can load the modules by:

module load biocontainers
module load srst2

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run srst2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=srst2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers srst2