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

Pierre-Alain Chaumeil; Aaron J Mussig; Philip Hugenholtz; Donovan H Parks

doi:10.1093/bioinformatics/btz848

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

Bioinformatics. 2019 Nov 15;36(6):1925-1927. doi: 10.1093/bioinformatics/btz848. Online ahead of print.

Authors

Pierre-Alain Chaumeil¹, Aaron J Mussig¹, Philip Hugenholtz¹, Donovan H Parks¹

Affiliation

¹ Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.

Abstract

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.