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