Dataset Information
GTDB-Tk v2: memory friendly classification with the genome taxonomy database.
Ontology highlight
ABSTRACT: 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.
SUBMITTER: Chaumeil PA
PROVIDER: S-EPMC9710552 | biostudies-literature | 2022 Nov
REPOSITORIES: biostudies-literature
Publications
GTDB-Tk v2: memory friendly classification with the genome taxonomy database.
Bioinformatics (Oxford, England) 20221101 23
<h4>Summary</h4>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 ...[more]