TaxonKit: A practical and efficient NCBI taxonomy toolkit

The National Center for Biotechnology Information (NCBI) Taxonomy is widely applied in biomedical and ecological studies. Typical demands include querying taxonomy identifier (TaxIds) by taxonomy names, querying complete taxonomic lineages by TaxIds, listing descendants of given TaxIds, and others....

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Bibliographic Details
Published inJournal of genetics and genomics Vol. 48; no. 9; pp. 844 - 850
Main Authors Shen, Wei, Ren, Hong
Format Journal Article
LanguageEnglish
Published China Elsevier Ltd 20.09.2021
Subjects
ancestry
Classification - methods
Computational Biology - methods
data collection
genomics
Lineage
National Center for Biotechnology Information
National Library of Medicine (U.S.)
NCBI Taxonomy
Software
TaxId
TaxId changelog
TaxonKit
taxonomy
United States
United States
TaxonKit
Lineage
NCBI Taxonomy
TaxId
TaxId changelog
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Summary:The National Center for Biotechnology Information (NCBI) Taxonomy is widely applied in biomedical and ecological studies. Typical demands include querying taxonomy identifier (TaxIds) by taxonomy names, querying complete taxonomic lineages by TaxIds, listing descendants of given TaxIds, and others. However, existed tools are either limited in functionalities or inefficient in terms of runtime. In this work, we present TaxonKit, a command-line toolkit for comprehensive and efficient manipulation of NCBI Taxonomy data. TaxonKit comprises seven core subcommands providing functions, including TaxIds querying, listing, filtering, lineage retrieving and reformatting, lowest common ancestor computation, and TaxIds change tracking. The practical functions, competitive processing performance, scalability with different scales of datasets and good accessibility can facilitate taxonomy data manipulations. TaxonKit provides free access under the permissive MIT license on GitHub, Brewsci, and Bioconda. The documents are also available at https://bioinf.shenwei.me/taxonkit/.
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ISSN:1673-8527
DOI:10.1016/j.jgg.2021.03.006