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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.

fastp

fastp is a tool designed to provide fast all-in-one preprocessing for FASTQ files. It performs adapter trimming, quality filtering, per-read quality pruning and generates quality-control reports in HTML and JSON.

License

Free to use and open source under the MIT License.

Available

  • Roihu: 1.0.1, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load fastp/1.0.1

For paired-end data:

fastp -i read1.fq.gz -I read2.fq.gz -o out1.fq.gz -O out2.fq.gz --thread 4

Example batch script

#!/bin/bash
#SBATCH --job-name=fastp
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=02:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load fastp/1.0.1

fastp -i read1.fq.gz -I read2.fq.gz -o out1.fq.gz -O out2.fq.gz --thread $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