resfinder
Link to section 'Introduction' of 'resfinder' Introduction
ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.
Home page: https://github.com/cadms/resfinder
Link to section 'Versions' of 'resfinder' Versions
- 4.1.5
Link to section 'Commands' of 'resfinder' Commands
- run_resfinder.py
- run_batch_resfinder.py
Link to section 'Module' of 'resfinder' Module
You can load the modules by:
module load biocontainers
module load resfinder
Link to section 'Example job' of 'resfinder' Example job
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 resfinder on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=resfinder
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers resfinder
run_resfinder.py -o output -db_res db_resfinder/ \
-db_res_kma db_resfinder/kma_indexing -db_point db_pointfinder/ \
-s "Escherichia coli" --acquired --point -ifq data/test_isolate_01_*