Mykrobe

Introduction

Mykrobe analyses the whole genome of a bacterial sample, all within a couple of minutes, and predicts which drugs the infection is resistant to.

For more information, please check:

Docker hub: https://hub.docker.com/r/staphb/mykrobe

Home page: https://github.com/Mykrobe-tools/mykrobe

Versions

• 0.11.0

Commands

• mykrobe

Module

You can load the modules by:

module load biocontainers
module load mykrobe

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 mykrobe on our clusters:

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

module --force purge
ml biocontainers mykrobe