CRISPRCasFinder

Introduction

CRISPRCasFinder enables the easy detection of CRISPRs and cas genes in user-submitted sequence data. It is an updated, improved, and integrated version of CRISPRFinder and CasFinder.

Detailed usage can be found here: https://github.com/dcouvin/CRISPRCasFinder

Versions

• 4.2.20

Commands

• CRISPRCasFinder.pl

Module

You can load the modules by:

module load biocontainers
module load crisprcasfinder/4.2.20

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 CRISPRCasFinder on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 2:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=CRISPRCasFinder
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers crisprcasfinder/4.2.20

CRISPRCasFinder.pl -in install_test/sequence.fasta -cas -cf CasFinder-2.0.3 -def G -keep