Software: Abricate
Description
Abricate is a tool for mass screening of contigs for antimicrobial resistance or virulence genes.
Available Versions
Unspecified: | 1.0.1 |
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For more information, please check its website: https://biocontainers.pro/tools/abricate and its home page on Github.
Versions
- 1.0.1
Commands
- abricate
Module
You can load the modules by:
module load biocontainers
module load abricate
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 Abricate on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=abricate
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers abricate
abricate --threads 8 *.fasta