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GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

Bioinformatics, 2019-11, Vol.36 (6), p.1925-1927 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press. 2019 ;The Author(s) 2019. Published by Oxford University Press. ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btz848 ;PMID: 31730192

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  • Title:
    GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
  • Author: Chaumeil, Pierre-Alain ; Mussig, Aaron J ; Hugenholtz, Philip ; Parks, Donovan H
  • Hancock, John
  • Subjects: Applications Note
  • Is Part Of: Bioinformatics, 2019-11, Vol.36 (6), p.1925-1927
  • Description: Abstract Summary The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk is computationally efficient and able to classify thousands of draft genomes in parallel. Here we demonstrate the accuracy of the GTDB-Tk taxonomic assignments by evaluating its performance on a phylogenetically diverse set of 10 156 bacterial and archaeal metagenome-assembled genomes. Availability and implementation GTDB-Tk is implemented in Python and licenced under the GNU General Public Licence v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk. Supplementary information Supplementary data are available at Bioinformatics online.
  • Publisher: England: Oxford University Press
  • Language: English
  • Identifier: ISSN: 1367-4803
    EISSN: 1460-2059
    EISSN: 1367-4811
    DOI: 10.1093/bioinformatics/btz848
    PMID: 31730192
  • Source: Oxford Journals Open Access Collection
    Journals@Ovid Open Access Journal Collection Rolling
    Geneva Foundation Free Medical Journals at publisher websites
    PubMed Central
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