coinfinder.rst

Coinfinder

Introduction ~~~~~~~~ Coinfinder is an algorithm and software tool that detects genes which associate and dissociate with other genes more often than expected by chance in pangenomes.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/coinfinder
Home page: https://github.com/fwhelan/coinfinder

Versions

• 1.2.0

Commands ~~~~~~~ - coinfinder

Module

You can load the modules by:

module load biocontainers
module load coinfinder

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 coinfinder on our clusters:

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

module --force purge
ml biocontainers coinfinder

coinfinder -i coinfinder-manuscript/gene_presence_absence.csv \
    -I -p coinfinder-manuscript/core-gps_fasttree.newick \
    -o output