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