Inquiry

[LanSabb]

Hi. Thanks for nice tool

I would like to ask the vOTU clustering.

I have large multi-contig viral sequences including both putative giant viruses and vOTUs not affiliated to putative giant viruses

If I run vOTU clustering based on "6.2. Assign viral contigs into vOTUs following MIUViG standards", I worry about the possibility that one of some multi-contig from giant viruses may collapse with other vOTUs

Do you think this can happen? If so, how am I supposed to deal with this problem??

Thanks !

[aziele]

Hi, thanks for the question and the kind words.

At the moment, Vclust does not handle multi-contig genomes. Each contig is clustered independently. Because of that, yes, it is possible that contigs from a multi-contig genome could cluster with other vOTUs, especially if they are short or highly similar to parts of other viruses. Handling multi-contig genomes properly is something we're adding in Vclust 2, planned for Q1 2026.

As a temporary workaround, you can concatenate contigs belonging to the same genome into a single sequence before running Vclust. This isn't ideal, but it prevents contigs from being split across vOTUs. Vclust is robust to genome rearrangements and relies on local similarities, so it should still recognize related viruses even if the contig order is artificial.