GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
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 GTD...
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| Published in | Bioinformatics Vol. 36; no. 6; pp. 1925 - 1927 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
15.11.2019
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| Subjects | |
| Online Access | Get full text |
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| Abstract | 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. |
|---|---|
| AbstractList | 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. 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.SUMMARYThe 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.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.AVAILABILITYGTDB-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 data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. 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. 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 data are available at Bioinformatics online. |
| Author | Mussig, Aaron J Hugenholtz, Philip Parks, Donovan H Chaumeil, Pierre-Alain |
| AuthorAffiliation | Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, Australia |
| AuthorAffiliation_xml | – name: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, Australia |
| Author_xml | – sequence: 1 givenname: Pierre-Alain surname: Chaumeil fullname: Chaumeil, Pierre-Alain email: p.chaumeil@uq.edu.au organization: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia – sequence: 2 givenname: Aaron J orcidid: 0000-0002-9988-0866 surname: Mussig fullname: Mussig, Aaron J organization: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia – sequence: 3 givenname: Philip surname: Hugenholtz fullname: Hugenholtz, Philip organization: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia – sequence: 4 givenname: Donovan H surname: Parks fullname: Parks, Donovan H email: donovan.parks@gmail.com organization: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31730192$$D View this record in MEDLINE/PubMed |
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| References | Nabhan (2023060912002093400_btz848-B13) 2012; 13 Kitts (2023060912002093400_btz848-B10) 2016; 44 Bowers (2023060912002093400_btz848-B3) 2017; 35 Konstantinidis (2023060912002093400_btz848-B11) 2005; 102 Coil (2023060912002093400_btz848-B4) 2019; 14 Matsen (2023060912002093400_btz848-B12) 2010; 11 Federhen (2023060912002093400_btz848-B6) 2015; 43 Pasolli (2023060912002093400_btz848-B17) 2019; 176 Rodriguez-R (2023060912002093400_btz848-B18) 2018; 46 Arkin (2023060912002093400_btz848-B2) 2018; 36 Hyatt (2023060912002093400_btz848-B8) 2010; 11 Parks (2023060912002093400_btz848-B15) 2018; 36 Parks (2023060912002093400_btz848-B14) 2017; 2 Eddy (2023060912002093400_btz848-B5) 2011; 7 Segata (2023060912002093400_btz848-B19) 2013; 4 Godfray (2023060912002093400_btz848-B7) 2002; 417 Jain (2023060912002093400_btz848-B9) 2017; 9 Parks (2023060912002093400_btz848-B16) 2019; 771964 Anantharaman (2023060912002093400_btz848-B1) 2016; 7 |
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Summary
The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the GTDB.... The GTDB Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB). GTDB-Tk is... |
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| Title | GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database |
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