Accuracy

The similarity of GTDB-Tk v1 and v2 classifications were first assessed using 16,710 bacterial genomes from the GEMs dataset (Nayfach et al., 2021) that represent novel taxa relative to GTDB R07-RS207. | Only 12 genomes (0.07%) did not have identical classifications between GTDB-Tk v1 and the divide-and-conquer approach used in GTDB-Tk v2. | The majority of incongruence was due to genomes being over- (6 genomes) or under-classified (4 genomes) by a single taxonomic rank. Only 2 genomes had conflicting taxonomic assignments, and these were both relatively poor-quality genomes assigned as new classes in alternative phyla.

Table 1. Novelty of GEM genomes relative to GTDB R07-RS207 based on GTDB-Tk v1 classifications.

		GTDB-Tk v2 classifications relative to GTDB-Tk v1 classifications
Toxon Novelty	No genomes	Congruent	Conflict	Underclassified	Overclassified
Novel phylum	3	2	0	0	1
Novel class	42	35	2	2	2
Novel order	144	143	0	0	1
Novel family	543	540	0	1	2
Novel genus	3,222	3,219	0	1	0
Novel species	12,756	12,756	0	0	0