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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