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

Pierre-Alain ChaumeilAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, AustraliaAaron J. MussigAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, AustraliaPhilip HugenholtzAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, AustraliaDonovan H. ParksAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, Australia

2019en

ABI

Annotatsiya

SUMMARY: The GTDB Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (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: GTDB-Tk is implemented in Python and licensed under the GNU General Public License v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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DOI: 10.1093/bioinformatics/btz848

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