Taxonomic assignment of virus genomes

geNomad is able to assign viral genomes to taxonomic lineages defined in ICTV’s VMR number 19. This is allowed by the 85,315 markers that are associated with viral taxa that cover most of the lineages recognized by the ICTV.

Taxonomic assignment algorithm

To assign viral sequences to specific taxa, geNomad first aligns the genes encoded by the sequences to a set of 227,897 markers. The genes that produce significant matches are then assigned to a marker, which might contain taxonomic information (colored genes below).

Each gene is subsequently classified based on the taxonomic lineage of the assigned marker. Different genes within the sequence might be assigned to different lineages.

To establish a single sequence-level taxonomy, weights are computed for each taxon included among the gene-level assignments, as well as their parent taxa (up to the root of the taxonomy) by summing the bitscores obtained from the alignments with marker profiles.

The taxonomy of the sequence is determined as the most specific taxon that is supported by at least 50% of the total weight (sum of the bitscores of all genes with taxonomy). In the example above, both families (Autographiviridae and Zobellviridae) failed to reach 50% consensus, so the genome is assigned to the class Caudoviricetes.

Final classification: Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes.