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

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ID: 289100
2018
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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.
Reference Key
openalex_W2951912016 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu
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Journal BMC Bioinformatics
Year 2018
DOI
10.1093/bioinformatics/bty560
URL
https://academic.oup.com/bioinformatics/article-pdf/34/17/i884/25702346/bty560.pdf
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