abricate
Link to section 'Introduction' of 'abricate' Introduction
Abricate is a tool for mass screening of contigs for antimicrobial resistance or virulence genes.
For more information, please check its website: https://biocontainers.pro/tools/abricate and its home page on Github.
Link to section 'Versions' of 'abricate' Versions
- 1.0.1
Link to section 'Commands' of 'abricate' Commands
- abricate
Link to section 'Module' of 'abricate' Module
You can load the modules by:
module load biocontainers
module load abricate
Link to section 'Example job' of '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