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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.

VSEARCH

VSEARCH is a versatile open-source tool for metagenomics. It offers fast searching, clustering, chimera detection, dereplication, subsampling and other operations on nucleotide sequences, and is a common open-source alternative to USEARCH.

License

Free to use and open source under GNU GPLv3.

Available

  • Roihu: 2.22.1, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load vsearch/2.22.1

For example, to cluster sequences at 97% identity:

vsearch --cluster_fast input.fasta --id 0.97 --centroids centroids.fasta --threads 8

Example batch script

#!/bin/bash
#SBATCH --job-name=vsearch
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load vsearch/2.22.1

vsearch --cluster_fast input.fasta --id 0.97 --centroids centroids.fasta --threads $SLURM_CPUS_PER_TASK

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