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September 12, 2025Open Access

fastp 1.0: An ultra‐fast all‐round tool for FASTQ data quality control and preprocessing

Key Points

Fastp 1.0 enhances FASTQ data quality control with new features and improved performance, showcasing significant advances over previous versions.
It outperformed Trimmomatic and Cutadapt in efficiency, demonstrating fastp's versatility as a robust preprocessing tool for bioinformatics.
The introduction of batch processing scripts enables users to handle multiple FASTQ files effectively, streamlining workflows in data analysis.
Software design principles were emphasized to underline how successful bioinformatics software can be developed while maintaining user-friendly features.

Abstract

Abstract Fastp has been recognized as one of the most popular FASTQ file preprocessors because of its powerful functions and extreme performance. As its first major update, fastp 1.0 will be formally presented in this paper, including its new features and the implementation principles behind it. Two other popular FASTQ preprocessors, Trimmomatic and Cutadapt, will be compared to demonstrate the great advantages of fastp in terms of simplicity, efficiency, and versatility. Some modules, such as the batch processing scripts, will be introduced on how to apply fastp to process FASTQ files efficiently. Additionally, some software design principles will be highlighted to showcase how to develop a successful bioinformatics software.

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