Circular virus identification

[xjhzjucas]

Hi developer, I'm curious about can genomad identify circular virus and how? Can I use the checkv trimmed sequence as input of geNomad? If so, would this affect the result of circular virus identification? Thank you so much!

[apcamargo]

A couple of things:

• The standard pipeline for virus identification would be geNomad → CheckV. Since CheckV is not meant for virus identification, it doesn't make much sense to run it before geNomad (unless you have a very specific use case in mind, of course).
• CheckV tries to trim out host genes on the edges of proviruses. So, if you had a sequence that was trimmed, it is probably not a circular virus (again, I don't really think you should use CheckV before geNomad).
• There are two types of complete viruses that we can easilt recognize in sequencing data: proviruses flanked by host on both sides and circular viruses with direct terminal repeats. geNomad will be able to identify both and they will be in the summary output files. You can read more about how to find such proviruses and sequences with direct terminal repeats here.

[xjhzjucas]

Thank you for your help! I'm sorry let me explain why I ask such a question, because I don't know how to use CheckV to identify circular virus so then I want to use genoamd instead to identify circular virus. In the result of checkv, I didn't find the information of circular virus and don't know what informations refer to.

[apcamargo]

In the summary file, just find the sequences with DTR in the topology column.

[xjhzjucas]

Thank you for your help!

[apcamargo]

No problem!