I am working on detection of mitochondrial DNA mutations. I have performed sequencing of mtDNA from mice, and am using MapSplice2 for further analysis.
I was getting some unexpected results (or rather, I was lacking some expected large deletions) with MapSplice2. I looked at the coverage across the mt genome, and found that the sequence coverage is dropping considerably at the ends of the mtDNA. Which of course in retrospect makes sense, as my circular genome is being handled as a linear one, which is probably causing problems in the mapping (MapSplice2 uses Bowtie)....
But what are the options for mappers that can handle circularity? I am familiar with STAR, but did not find any information on it supporting circular genomes.