fastp: an ultra-fast all-in-one FASTQ preprocessor

TLDR

Quality control and preprocessing of FASTQ files are essential for clean downstream data, yet traditional tools are slow because they are written in high‑level languages and lack efficient multithreading. We developed fastp as an ultra‑fast FASTQ preprocessor that integrates quality control, adapter trimming, and data filtering into a single tool. Written in C++ with multi‑threading, fastp performs all QC, trimming, filtering, and per‑read pruning in a single scan of the FASTQ data. Fastp is 2–5× faster than Trimmomatic or Cutadapt while offering more features, and its open‑source code is available on GitHub.

Abstract

Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient.We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2-5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools.The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.