I have sequenced a virus genome using Illumina. As viruses are evolving rapidly, I suspect that there is more than one genotype in my "pure" sample - one dominant and many satellite genotypes. When I sequenced a batch of viruses I have a crazy coverage of more than 10,000X for some of them. So, I am wondering if it is possible to look at the alignment of the reads to the assemblies to find possible Hot Spots that accumulate mutations.
Which program/algorithm should I use to address this question ?
Any comments/suggestions are welcome.