【摘 要】
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The National Center for Biotechnology Information (NCBI) Taxonomy is widely applied in biomedical and ecological studies.Typical demands include querying taxonomy identifier (Taxlds) by taxonomy names,querying complete taxonomic lineages by Taxlds,listing
【机 构】
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Institute for Viral Hepatitis,Department of Infectious Diseases,Key Laboratory of Molecular Biology
论文部分内容阅读
The National Center for Biotechnology Information (NCBI) Taxonomy is widely applied in biomedical and ecological studies.Typical demands include querying taxonomy identifier (Taxlds) by taxonomy names,querying complete taxonomic lineages by Taxlds,listing descendants of given Taxlds,and others.How-ever,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 Taxlds querying,listing,filtering,lineage retrieving and reformatting,lowest common ancestor computation,and Taxlds 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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