TaxonKit:A practical and efficient NCBI taxonomy toolkit

作     者：Wei Shen Hong Ren Wei Shen;Hong Ren

作者机构：Institute for Viral HepatitisDepartment of Infectious DiseasesKey Laboratory of Molecular Biology for Infectious DiseasesMinistry of EducationThe Second Affiliated Hospital of Chongqing Medical UniversityChongqing 400010China 

出 版 物：《Journal of Genetics and Genomics》 (遗传学报（英文版）)

年 卷 期：2021年第48卷第9期

页      面：844-850页

核心收录：

学科分类：0710[理学-生物学] 0711[理学-系统科学] 07[理学] 1001[医学-基础医学(可授医学、理学学位)] 

基　　金：supported by grants from the National Natural Science Foundation of China(32000474)to W.S the National Science and Technology Major Project of China(2017ZX10202203-007-001)to H.R. 

主　　题：NCBI Taxonomy TaxonKit TaxId Lineage TaxId changelog 

摘      要：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.***.me/taxonkit/.