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

By Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz, Donovan H. Parks. Bioinform., 2019

4,714 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3aca912f21d54b3931fa1fdfac0c199c557374a4

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Citations in the corpus

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria (2023, neutral): “5.0 (default parameters; [40]).”
EzBioCloud: a genome-driven database and platform for microbiome identification and discovery (2024, positive): “Finally, we validated the taxonomic placement using GTDB-tk [15], following their taxonomic nomenclature up to genus level.”
Effect of ammonia on anaerobic digestion of municipal solid waste: Inhibitory performance, bioaugmentation and microbiome functional reconstruction (2020, positive): “GTDB-Tk [40] and CAT [41] provided taxonomical assignment and functional analysis.”
DRAM for distilling microbial metabolism to automate the curation of microbiome function (2020, methodology): “Genomes were quality checked with checkM (51) and taxonomically classified using GTDB-Tk (v0.”
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2020, background): “These efforts have also led to increased consistency in microbial systematics and phylogeny, facilitating the types of automated, high-throughput analyses necessary when manual curation cannot keep up with such rapid growth (Asnicar et al., 2020; Chaumeil et al., 2019) .”
GTDB-Tk v2: memory friendly classification with the genome taxonomy database (2022, methodology): “A primary step in assigning classifications is placing genomes into the GTDB bacterial or archaeal reference trees using the maximum likelihood (ML) placement tool pplacer (Matsen et al. 2010).”
Polypolish: Short-read polishing of long-read bacterial genome assemblies (2021, neutral): “The six bacterial isolates used in the real-read tests each belong to a different species: Acinetobacter baumannii , Citrobacter koseri , Enterobacter kobei , an unnamed Haemophilus species (given the placeholder name Haemophilus sp002998595 in GTDB R202 [28, 29]), Klebsiella oxytoca and Klebsiella ”
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy (2021, background): “Use of these quantitative criteria for circumscribing taxa allows for automated classification of new genomes (6), ensures all genomes are classified from species to domain, and normalizes the definition of taxonomic ranks across the bacterial and archaeal domains.”