defective viral genomes (DVGs)

[abrozzi]

Dear breseq team,

thank you for your great work on breseq.

I recently transitioned from microbial genomics to some viral genomics, specifically on the detection of Defective Viral Genomes (DVGs). As an example of this type of analysis, here is a recent preprint: https://www.biorxiv.org/content/10.64898/2026.03.11.711002v1.

I was wondering whether you think deletions in viral genome sequencing data could be detected using breseq.

Have you ever considered extending breseq to support viral genome analyses?

Thank you

-A

[jeffreybarrick]

There's no reason you can't run viral genome sequencing data through breseq. It's been used for a number of projects with phages. It should be able to detect deletions in viral genomes, esp. if they create new sequence junctions.

If your viral genome sequencing datasets have extremely high sequencing depth, this could slow/complicate some things, so you might want to limit the coverage you use (-l option).

One thing that may obscure deletions: if you have just a few spurious reads covering the deletion in a sample such that its coverage never goes to zero at any position, a missing coverage evidence item will not be seeded and predicted. (We have some improved copy number variation prediction code that we are hoping to integrate soon that would make things more robust to this case where just a few reads misassigned to the wrong sample can cause a problem.)

The usual caveat of having many false-positive mutation predictions in population (metagenomic) sequencing data also applies. You'd need to add some additional stats for filtering these predictions if you are analyzing this type of sample.