I am working on tracking and tracing of viruses in plant seed lots. I have total RNAseq data from the seed lots (around 200 samples). I did a kraken2 analysis to fish out certain viruses which we are interested in. For each seed lots, I have the total reads for a given species of viruses. How to I see if for a given seedlot, if there are multiple strains ? I would also like to do the strain level analysis across multiple seedlots. Any idea which tools or what kind of analysis/visualization I could go for ? It can get complicated especially because I have 200 samples.