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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Detalles Bibliográficos
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
Descripción
Sumario: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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