coinfinder
Link to section 'Introduction' of '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.
BioContainers: https://biocontainers.pro/tools/coinfinder
Home page: https://github.com/fwhelan/coinfinder
Link to section 'Versions' of 'coinfinder' Versions
- 1.2.0
Link to section 'Commands' of 'coinfinder' Commands
- coinfinder
Link to section 'Module' of 'coinfinder' Module
You can load the modules by:
module load biocontainers
module load coinfinder
Link to section 'Example job' of 'coinfinder' 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 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