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bioRxiv · 10.1101/2022.07.11.499641

GTDB-Tk v2: memory friendly classification with the Genome Taxonomy Database

Chaumeil, P.-A.·Mussig, A. J.·Hugenholtz, P.·Parks, D. H.
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Abstract

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. AvailabilityGTDB-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. Contactp.chaumeil@uq.edu.au or donovan.parks@gmail.com

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Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P., Parks, D. H.. 2022-07-22. GTDB-Tk v2: memory friendly classification with the Genome Taxonomy Database. https://doi.org/10.1101/2022.07.11.499641

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