Using Salmon to maps reads from different SARS2 virus variants

[maximus-sci]

I'm looking at sequencing from cells infected with different SARS2 virus variants. In addition to looking at the host transcriptome, I'd also like to know more about the different levels of viral transcript expression. I'm curious the best way to do this. I can very easily take the SARS2 reference strain and generate a combined human-SARS2 transcriptome, but I'm worried about how the various mutations that define these viral strains will mess with Salmon's mapping of reads.

My current plan is to drop the --minScoreFraction (maybe to 0.7?) and change the mismatch penalty to 0, but I'm not sure it's the best option. I could also try to hunt down the genomes of each variant I'm using, but the annotations and deposited sequences for a lot of the variants aren't super great, so I might just run into this same problem.

Any advice on how best to use Salmon for this task would be greatly appreciated!