Pilon

Introduction

Pilon is an automated genome assembly improvement and variant detection tool.

For more information, please check its website: https://biocontainers.pro/tools/pilon and its home page on Github.

Versions

1.24

Commands

pilon.jar

Module

You can load the modules by:

module load biocontainers
module load pilon

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 Pilon on our clusters:

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

module --force purge
ml biocontainers pilon

pilon.jar --nostrays \
     --genome scaffolds.fasta \
     --frags out_sorted.bam \
     --vcf --verbose --threads 12 \
     --output pilon_corrected \
     --outdir pilon_outdir