fastp Tutorial: Fast FASTQ Preprocessing & Quality Control

Last updated: March 13, 2026

Introduction

Raw data from next-generation sequencers (FASTQ files) often contains reads with adapter sequences and reads of poor quality. Before proceeding with downstream analyses, you need to trim adapter sequences and filter out low-quality reads from your FASTQ files.

fastp is one of the tools available for preprocessing FASTQ files. While other preprocessing tools exist, fastp is particularly fast because it is written in C++ and supports multithreading.

Installing fastp

On CentOS or Ubuntu, you can install fastp with the following commands.

$ wget http://opengene.org/fastp/fastp $ chmod a+x ./fastp

On macOS, running the binary downloaded above may produce the following error.

./fastp: cannot execute binary file

In that case, you can install fastp through Bioconda instead.

$ conda install -c bioconda fastp

Try displaying the help message to verify the installation.

$ fastp --help

If you see output similar to the following, the installation was successful.

usage: fastp [options] ... options: -i, --in1 read1 input file name (string [=]) -o, --out1 read1 output file name (string [=]) -I, --in2 read2 input file name (string [=]) -O, --out2 read2 output file name (string [=]) -D, --dedup enable deduplication to drop the duplicated reads/pairs...

Running Preprocessing

For single-end reads, run the following command to preprocess your data.

$ fastp -i raw.fastq -o filtered.fastq.gz

For paired-end reads, use the following command instead.

$ fastp -i raw_1.fastq -I raw_2.fastq -o filtered_1.fastq.gz -O filtered_2.fastq.gz

The preprocessed FASTQ files are output in GZIP-compressed format.

fastp also generates an HTML report like the one shown below.

You can view a full sample report here.

RNA-Seq Data Analysis Software

This is an RNA-Seq Data Analysis Software recommended for those who:

✔︎ Seeking to avoid outsourcing or collaboration for RNA-Seq data analysis.

✔︎ Lacking time to learn RNA-Seq data analysis.

✔︎ Frustrated by the complexity of existing tools.

Users can perform gene expression quantification, identification of differentially expressed genes, gene ontology(GO) analysis, pathway analysis, as well as drawing volcano plots, MA plots, and heatmaps.

About the Author

BxINFO LLC

A research support company specializing in bioinformatics.

We provide tools and information to support life science research, with a focus on RNA-Seq analysis.

→ Learn more

Recommended Pages