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

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 tax...

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Autores principales: Chaumeil, Pierre-Alain, Mussig, Aaron J, Hugenholtz, Philip, Parks, Donovan H
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7703759/
https://www.ncbi.nlm.nih.gov/pubmed/31730192
http://dx.doi.org/10.1093/bioinformatics/btz848
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author Chaumeil, Pierre-Alain
Mussig, Aaron J
Hugenholtz, Philip
Parks, Donovan H
author_facet Chaumeil, Pierre-Alain
Mussig, Aaron J
Hugenholtz, Philip
Parks, Donovan H
author_sort Chaumeil, Pierre-Alain
collection PubMed
description 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.
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spelling pubmed-77037592020-12-07 GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database Chaumeil, Pierre-Alain Mussig, Aaron J Hugenholtz, Philip Parks, Donovan H Bioinformatics Applications Note 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. Oxford University Press 2020-03-15 2019-11-15 /pmc/articles/PMC7703759/ /pubmed/31730192 http://dx.doi.org/10.1093/bioinformatics/btz848 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Chaumeil, Pierre-Alain
Mussig, Aaron J
Hugenholtz, Philip
Parks, Donovan H
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
title GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
title_full GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
title_fullStr GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
title_full_unstemmed GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
title_short GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
title_sort gtdb-tk: a toolkit to classify genomes with the genome taxonomy database
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7703759/
https://www.ncbi.nlm.nih.gov/pubmed/31730192
http://dx.doi.org/10.1093/bioinformatics/btz848
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