Staramr

Introduction

staramr scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes.

For more information, please check:

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

Home page: https://github.com/phac-nml/staramr

Versions

• 0.7.1

Commands

• staramr

Module

You can load the modules by:

module load biocontainers
module load staramr

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 staramr on our clusters:

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

module --force purge
ml biocontainers staramr

staramr db info
staramr search \
    --pointfinder-organism salmonella \
    -o out *.fasta