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

Bioinformatics, 2018-09, Vol.34 (17), p.i884-i890 [Peer Reviewed Journal]

The Author(s) 2018. Published by Oxford University Press. 2018 ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/bty560 ;PMID: 30423086

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  • Title:
    fastp: an ultra-fast all-in-one FASTQ preprocessor
  • Author: Chen, Shifu ; Zhou, Yanqing ; Chen, Yaru ; Gu, Jia
  • Subjects: Eccb 2018: European Conference on Computational Biology Proceedings
  • Is Part Of: Bioinformatics, 2018-09, Vol.34 (17), p.i884-i890
  • Description: Abstract Motivation 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. Results 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. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
  • Publisher: England: Oxford University Press
  • Language: English
  • Identifier: ISSN: 1367-4803
    EISSN: 1460-2059
    EISSN: 1367-4811
    DOI: 10.1093/bioinformatics/bty560
    PMID: 30423086
  • Source: Oxford Journals Open Access Collection
    Journals@Ovid Open Access Journal Collection Rolling
    PubMed Central (Open access)
    Geneva Foundation Free Medical Journals at publisher websites
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