GTDB-Tk v2: memory friendly classification with the genome taxonomy database

By Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz, Donovan H. Parks. bioRxiv, 2022

1,663 citations recorded by the source corpus.

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 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. Contact p.chaumeil@uq.edu.au or donovan.parks@gmail.com

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1920ce7b92dccf013b8158c80d86c1e960bf0b00