Jellyfish

JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. It can count k-mers using an in-memory hash table and is commonly used for genome-size estimation and other k-mer based analyses.

Jellyfish

License

Free to use and open source under GNU GPLv3.

Available

Roihu: 2.2.7, via the bio-apps module.

Usage

Jellyfish is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Jellyfish module:

module load bio-apps/v202603
module load jellyfish/2.2.7

Count k-mers (here 21-mers) and generate a histogram:

jellyfish count -m 21 -s 100M -t 8 -C reads.fasta -o mer_counts.jf
jellyfish histo mer_counts.jf > mer_counts.histo

Example batch script

#!/bin/bash
#SBATCH --job-name=jellyfish
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=02:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load jellyfish/2.2.7

jellyfish count -m 21 -s 100M -t $SLURM_CPUS_PER_TASK -C reads.fasta -o mer_counts.jf

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk