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