Taxonomic information

[YumengYan]

Thanks for sharing the protocol. I have tried it for some prophage genomes, but most genomes can only have the taxonomic information in "class" level. Is there a way to get species/family level information?

[apcamargo]

That's probably because most prophages will be Caudoviricetes and most can't be assigned to a particular family. That's expected.

If you want more details, you can try to use geNomad for taxonomic assignment. It will tell you the taxonomy assigned to each gene. But I wouldn't expect significant changes.