The Genome Taxonomy Database (GTDB) is a database that provides a set of high quality microbial genomes with standardised taxonomic assignments derived from phylogenetics as a reference for the taxonomic assignment of new species. The entire database of genomes is available for performing large scale genomic analyses on high-quality, taxonomically annotated genomes.
Also available is the GTDB-tk tool for the taxonomic assignment of new genomes from sequence data from this github repository.
GTDB: Parks, D.H., et al. (2021). GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research, 50: D785–D794.
GTDB-tk: Chaumeil PA, et al. 2022. GTDB-Tk v2: memory friendly classification with the Genome Taxonomy Database. Bioinformatics, btac672.