Software: staramr
Description
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.
Available Versions
| Unspecified: | 0.7.1 |
|---|
Docker hub: https://hub.docker.com/r/staphb/staramr
Home page: https://github.com/phac-nml/staramr
Commands
- staramr
Module
You can load the modules by:
module load biocontainers
module load staramr
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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