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

Chen, S.; Zhou, Y.; Chen, Y.; Gu, J.

doi:10.1101/274100

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bioRxiv · 10.1101/274100

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

Chen, S.·Zhou, Y.·Chen, Y.·Gu, J.

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Abstract

MotivationQuality 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.\n\nResultsWe 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 cutting, and many other operations with a single scan of the FASTQ data. It also supports unique molecular identifier preprocessing, poly tail trimming, output splitting, and base correction for paired-end data. It can automatically detect adapters for single-end and paired-end 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.\n\nAvailability and ImplementationThe open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp\n\nContactchen@haplox.com

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Chen, S., Zhou, Y., Chen, Y., Gu, J.. 2018-03-01. fastp: an ultra-fast all-in-one FASTQ preprocessor. https://doi.org/10.1101/274100

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