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

By Wei Shen, Shuai Le, Yan Li, F. Hu. PLoS ONE, 2016

2,824 citations recorded by the source corpus.

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.

Subfields: Computer Networks and Communications, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/4f55d6d95090c46b65d40ca3ea027d6113a381d6

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Citations in the corpus

Petabase-scale sequence alignment catalyses viral discovery (2020, methodology): “15) was used for working with fasta files 56 .”
CPGView: A package for visualizing detailed chloroplast genome structures (2023, methodology): “The starting point of the chloroplast genome was adjusted using seqkit (version 0.12.1) (Shen et al., 2016), and the depth of coverage was detected using bwa (version 0.7.17) (Li & Durbin, 2010) and samtools software (version 0.1.19) (Li et al., 2009).”
Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs (2022, neutral): “QUAST [13], SeqKit [14] and Bandage [8].”
SeqKit2: A Swiss army knife for sequence and alignment processing (2024, methodology): “Some existing utilities, including Bioawk [1], Seqtk [2], BBMaps [3], and SeqKit [4], are widely used by bioinformatic researchers and have wide popularity for years at online question ‐ and ‐ answer platforms, such as BioStar [5].”
Gaia: An AI-enabled genomic context–aware platform for protein sequence annotation (2025, unknown): “A random set of 3000 proteins was selected from OG_prot90 using the seqkit sample function ( 54 ).”