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Pierre-Alain Chaumeil, Aaron James Mussig, Philip Hugenholtz, Donovan H. Parks
SUMMARY: The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, the growing size of the GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts of memory (∼320 GB) which limits its adoption and ease of use. Here, we present an update to GTDB-Tk that uses a divide-and-conquer approach where user genomes are initially placed into a bacterial reference tree with family-level representatives followed by placement into an appropriate class-level subtree comprising species representatives. This substantially reduces the memory requirements of GTDB-Tk while having minimal impact on classification. 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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Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2022). GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics, 38(23), 5315–5316. https://doi.org/10.1093/bioinformatics/btac672
Chaumeil, Pierre-Alain, et al. "GTDB-Tk v2: memory friendly classification with the genome taxonomy database." Bioinformatics, vol. 38, no. 23, 2022, pp. 5315–5316, https://doi.org/10.1093/bioinformatics/btac672.
Chaumeil, Pierre-Alain, Aaron James Mussig, Philip Hugenholtz, and Donovan H. Parks. "GTDB-Tk v2: memory friendly classification with the genome taxonomy database." Bioinformatics 38, no. 23 (2022): 5315–5316. https://doi.org/10.1093/bioinformatics/btac672.
Chaumeil P.-A., Mussig A. J., Hugenholtz P. [и др.] GTDB-Tk v2: memory friendly classification with the genome taxonomy database // Bioinformatics. — 2022. — Vol. 38, № 23. — P. 5315–5316. — URL: https://doi.org/10.1093/bioinformatics/btac672
@article{chaumeil2022gtdbtk,
title = {{GTDB-Tk v2: memory friendly classification with the genome taxonomy database}},
author = {Pierre-Alain Chaumeil and Aaron James Mussig and Philip Hugenholtz and Donovan H. Parks},
journal = {Bioinformatics},
year = {2022},
volume = {38},
number = {23},
pages = {5315--5316},
doi = {10.1093/bioinformatics/btac672},
url = {https://doi.org/10.1093/bioinformatics/btac672}
}TY - JOUR AU - Chaumeil, Pierre-Alain AU - Mussig, Aaron James AU - Hugenholtz, Philip AU - Parks, Donovan H. TI - GTDB-Tk v2: memory friendly classification with the genome taxonomy database JO - Bioinformatics VL - 38 IS - 23 SP - 5315 EP - 5316 PY - 2022 DA - 2022/10/07 DO - 10.1093/bioinformatics/btac672 UR - https://doi.org/10.1093/bioinformatics/btac672 ER -
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