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

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Chaumeil, Pierre-Alain, Mussig, Aaron J, Hugenholtz, Philip, Parks, Donovan H·2020·Bioinformatics
DOI 10.1093/bioinformatics/btz848
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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.

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Research works printed but not linked: 17

  1. Anantharaman, 2016, Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system, Nat. Commun, 7, 13219, 10.1038/ncomms13219 · DOI · Paper page
  2. Arkin, 2018, KBase: the United States Department of Energy Systems Biology Knowledgebase, Nat. Biotechnol, 36, 566, 10.1038/nbt.4163 · doi:10.1038/nbt.4163
  3. Bowers, 2017, Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea, Nat. Biotechnol, 35, 725, 10.1038/nbt.3893 · DOI · Paper page
  4. Coil, 2019, Genomes from bacteria associated with the canine oral cavity: a test case for automated genome-based taxonomic assignment, PLoS One, 14, e0214354, 10.1371/journal.pone.0214354 · DOI
  5. Federhen, 2015, Type material in the NCBI Taxonomy Database, Nucleic Acids Res, 43, D1086, 10.1093/nar/gku1127 · DOI · Paper page
  6. Godfray, 2002, Challenges for taxonomy, Nature, 417, 17, 10.1038/417017a · DOI · Paper page
  7. Hyatt, 2010, Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, 11, 119, 10.1186/1471-2105-11-119 · DOI · Paper page
  8. Kitts, 2016, Assembly: a resource for assembled genomes at NCBI, Nucleic Acids Res, 44, D73, 10.1093/nar/gkv1226 · DOI · Paper page
  9. Konstantinidis, 2005, Genomic insights that advance the species definition for prokaryotes, Proc. Natl. Acad. Sci. USA, 102, 2567, 10.1073/pnas.0409727102 · DOI · Paper page
  10. Matsen, 2010, pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree, BMC Bioinformatics, 11, 538, 10.1186/1471-2105-11-538 · DOI · Paper page
  11. Nabhan, 2012, The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy, Brief. Bioinform, 13, 122, 10.1093/bib/bbr014 · DOI · Paper page
  12. Parks, 2017, Recovery of nearly 8, 000 metagenome-assembled genomes substantially expands the tree of life, Nat. Microbiol, 2, 1533, 10.1038/s41564-017-0012-7 · DOI · Paper page
  13. Parks, 2018, A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life, Nat. Biotechnol, 36, 996, 10.1038/nbt.4229 · DOI · Paper page
  14. Parks, 2019, Selection of representative genomes for 24, 706 bacterial and archaeal species clusters provide a complete genome-based taxonomy, bioRxiv, 771964
  15. Pasolli, 2019, Extensive unexplored human microbiome diversity revealed by over 150, 000 genomes from metagenomes spanning age, geography, and lifestyle, Cell, 176, 649, 10.1016/j.cell.2019.01.001 · DOI · Paper page
  16. Rodriguez-R, 2018, The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of archaea and bacteria at the whole genome level, Nucleic Acids Res, 46, W282, 10.1093/nar/gky467 · DOI · Paper page
  17. Segata, 2013, PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes, Nat. Commun, 4, 2304, 10.1038/ncomms3304 · DOI · Paper page

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Metadata

Authors
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P., & Parks, D. H.
Venue
Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2019-11-15
Volume
36
Issue
6
Pages
1925-1927
ISSN
  • 1367-4803 (ISSN-L)
  • 1367-4811
DOI
10.1093/bioinformatics/btz848
OpenAlex
W2986925300
Cited by
5,259
References
2
FWCI
109.64
Type
journal article
Language
en
Open access
hybrid
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
Australian Research Council Laureate Fellowship (FL150100038)

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CoChat. (2026). Citation check: GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. https://app.cochat.ai/papers/10.1093/bioinformatics/btz848
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Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2020). GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz848

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