How do i create a `mm10_viral` reference?

[kopardev]

Is it possible to build our own mouse + mouse_viruses reference? If yes, how?

[jluebeck]

Hi Vishal,

Definitely possible and not too difficult. I can generate this in the next couple of weeks and include the usage option in our next release of the tool, around the same time. I'll keep you posted when it might be ready for testing.

Just to confirm, is the viral sequence you are interested in already in the set of viral genomes included with GRCh38, or did you have some other viral sequences in mind?

The viral genomes included in GRCh38_viral are derived from the ViFi publication (see section Methods: "Viral reference genomes"). Broadly, these are the papilloma and hepatitis viral sequences that are available from PaVE as well as from https://genome.cshlp.org/content/22/4/593.full. Supplementary Table 1 of the ViFi paper contains the relevant identifiers.

Thanks,
Jens