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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.

Mash

Mash is a fast tool for estimating the distance between genomes and metagenomes using the MinHash dimensionality-reduction technique. It reduces large sequences to compact sketches, enabling rapid distance and containment estimates.

License

Free to use and open source. See the Mash license.

Available

  • Roihu: 2.3, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load mash/2.3

Create sketches and estimate the distance between two genomes:

mash sketch -o reference genome1.fa
mash dist reference.msh genome2.fa

Example batch script

#!/bin/bash
#SBATCH --job-name=mash
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load mash/2.3

mash sketch -p $SLURM_CPUS_PER_TASK -o reference *.fa

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

More information