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
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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