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

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  • Pierre-Alain Chaumeil
    Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, Australia
  • Aaron J Mussig
    Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, Australia
  • Philip Hugenholtz
    Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, Australia
  • Donovan H Parks
    Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, Australia
  • John Hancock
    editor

Description

<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Summary</jats:title> <jats:p>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.</jats:p> </jats:sec> <jats:sec> <jats:title>Availability and implementation</jats:title> <jats:p>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.</jats:p> </jats:sec> <jats:sec> <jats:title>Supplementary information</jats:title> <jats:p>Supplementary data are available at Bioinformatics online.</jats:p> </jats:sec>

Journal

  • Bioinformatics

    Bioinformatics 36 (6), 1925-1927, 2019-11-15

    Oxford University Press (OUP)

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