GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.
basic_science · Level V
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- Record sourced from PubMed, PMID 31730192.
- Also identified by DOI 10.1093/bioinformatics/btz848 and PMC identifier 7703759.
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Abstract
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.