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.

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

License

Free to use and open source under the MIT License.

Available

• Roihu-CPU: 1.0.1, 1.3.6, 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/1.3.6

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/1.3.6

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

• fastp GitHub repository

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