Question about Checkm2 Annotation

[aljazdzy]

Is the Diamond output file the annotation of the entire bin or is it the annotation of specific genes that checkm2 considers important for things like completeness/contamination calculations?

[chklovski]

Hi, diamond annotation is of all genes, producing any KEGG annotations in its reference diamond database of uniref100 proteins with KEGG IDs. The ML models then determine the relevance of the presence, absence and counts of each of these genes.