Detection of eukaryotic viruses?

[rprops]

Is there any information on the performance/ability of VirSorter to detect signatures of eukaryotic viruses in environmental datasets? I've been playing a bit with the software but the output appears to be restricted to phage detection. In case not, any recommendations for a software that would be enable this?
Thanks,
Ruben

[simroux]

Hi Ruben,
Eukaryotic viruses are not well handled by VirSorter, they will typically show up in Categories 3 or 6 because of low proportion of genes with a hit in PFAM (that's what happens for instance for a lot of giant viruses and phycodnaviridae), or will not be detected at all.
For automatic detection of eukaryotic viruses in environmental datasets, this kind of depends on the type of eukaryotic viruses you are after, but typically I'd recommend working with marker genes of the viral group you are interested in. For instance, RdRP is a great marker gene for eukaryotic RNA viruses (and RNA phages as well). If you are interested in more of the larger viruses (Giant viruses, Phycodnaviridae), you can look into some recent paper including ours (https://www.nature.com/articles/s41586-020-1957-x) and other (https://www.nature.com/articles/s41467-020-15507-2), but it's typically (i) detecting candidate contigs / bins based on HMM of marker genes, then (ii) clean up these candidates by removing contigs / bins that are microbial. Unfortunately, I don't know of a software that would do this automatically.

Hope that helps !
Best,
Simon

[rprops]

Hi Simon,
This helps a lot - thanks for providing context and advice! Much appreciated!
Ruben