Resfinder

Introduction

ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.

For more information, please check:
Home page: https://github.com/cadms/resfinder

Versions

  • 4.1.5

Commands

  • run_resfinder.py

  • run_batch_resfinder.py

Module

You can load the modules by:

module load biocontainers
module load resfinder

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 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_*