Jellyfish

Introduction

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence.

For more information, please check its website: https://biocontainers.pro/tools/kmer-jellyfish and its home page: http://www.genome.umd.edu/jellyfish.html.

Versions

• 2.3.0

Commands

• jellyfish

Module

You can load the modules by:

module load biocontainers
module load kmer-jellyfish

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 Jellyfish on our clusters:

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

module --force purge
ml biocontainers kmer-jellyfish

jellyfish count -m 16 -s 100M -t 12 \
     -o mer_counts -c 7  input.fastq