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SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

Author

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  • Wei Shen
  • Shuai Le
  • Yan Li
  • Fuquan Hu

Abstract

FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. This paper describes a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing. SeqKit provides executable binary files for all major operating systems, including Windows, Linux, and Mac OSX, and can be directly used without any dependencies or pre-configurations. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. SeqKit is open source and available on Github at https://github.com/shenwei356/seqkit.

Suggested Citation

  • Wei Shen & Shuai Le & Yan Li & Fuquan Hu, 2016. "SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation," PLOS ONE, Public Library of Science, vol. 11(10), pages 1-10, October.
    • Handle: RePEc:plo:pone00:0163962
    DOI: 10.1371/journal.pone.0163962
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    Cited by:

    1. Edoardo Morandi & Matteo Cereda & Danny Incarnato & Caterina Parlato & Giulia Basile & Francesca Anselmi & Andrea Lauria & Lisa Marie Simon & Isabelle Laurence Polignano & Francesca Arruga & Silvia De, 2019. "HaTSPiL: A modular pipeline for high-throughput sequencing data analysis," PLOS ONE, Public Library of Science, vol. 14(10), pages 1-9, October.

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