Meryl

Introduction

Meryl is a genomic k-mer counter (and sequence utility) with nice features.

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

Versions

  • 1.3

Commands

  • meryl

  • meryl-analyze

  • meryl-import

  • meryl-lookup

  • meryl-simple

Module

You can load the modules by:

module load biocontainers
module load meryl

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 Meryl on our clusters:

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

module --force purge
ml biocontainers meryl

meryl count k=42 data/ec.fna.gz output ec.meryl