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.

• FASTX-Toolkit
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

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

• FASTX-Toolkit home page

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.