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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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.

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

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