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.

• VSEARCH
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

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

• VSEARCH GitHub repository

Do you find this page useful?

Yes

Thank you for your feedback!

No

Thank you! Your feedback is appreciated.

Please let us know how we could improve this page by contacting us or by creating an issue in GitHub. You can also edit this page yourself and contribute your improvements by creating a pull request.