inquiry on result intepretation

[LanSabb]

Hi

Genomad produces my test-run result

I am likely to deem the contigs as viral sequences if virus_score > 0.95, however most of the results were fully lacked of viral marker genes in the absence of terminal repeats (Note that input is metagenome contigs)

So am I supposed deem them as virus or not ??

Thanks

seq_name length topology coordinates n_genes genetic_code virus_score fdr n_hallmarks marker_enrichment taxonomy NODE_29377_length_4358_cov_3.390937 4358 No terminal repeats NA 6 11 0.9799 NA 0 6.2650 Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; NODE_8524_length_8796_cov_3.322870 8796 No terminal repeats NA 9 11 0.9686 NA 0 6.4393 Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; NODE_24214_length_4873_cov_2.848136 4873 No terminal repeats NA 2 11 0.9429 NA 1 3.4080 Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; NODE_16753_length_6014_cov_2.545055 6014 No terminal repeats NA 6 11 0.7747 NA 0 1.6963 Viruses;Varidnaviria;Bamfordvirae;Nucleocytoviricota;Megaviricetes;Imitervirales;Mimiviridae

[apcamargo]

Unfortunately, it's not straightforward. These can be sequences with genes that are enriched in viruses, but this doesn't necessarily mean that they are viruses.

Have you taken a look at the <prefix>_genes.tsv file to check which annotations you find? Can you share the genes of these sequences?