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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.

FASTX-Toolkit

The FASTX-Toolkit is a collection of command line tools for preprocessing short-read FASTA/FASTQ files. It includes tools such as fastx_trimmer, fastq_quality_filter, fastx_clipper and fastx_collapser.

License

Free to use and open source under GNU AGPLv3.

Available

  • Roihu: 0.0.14, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load fastx-toolkit/0.0.14

For example, to trim reads to a fixed length:

fastx_trimmer -l 50 -i input.fastq -o trimmed.fastq

or to filter by quality:

fastq_quality_filter -q 20 -p 80 -i input.fastq -o filtered.fastq

Example batch script

#!/bin/bash
#SBATCH --job-name=fastx
#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=1
#SBATCH --mem=2G

module load bio-apps/v202603
module load fastx-toolkit/0.0.14

fastx_trimmer -l 50 -i input.fastq -o trimmed.fastq

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