I am looking to map sequencing reads to a circular reference genome (animal mitochondrial genome in my case). I have been looking for an up-to-date tool that can map reads to a circular genome but have not been able to find one - does anyone know of a tool that can do this?
All answers I have found so far just recommend converting the circular reference into a linear sequence and simply mapping the reads as though it were a linear genome, with or without padding the ends of the reference to accommodate mapping reads on the very end. However, my purpose is to analyze the relative sequencing depth across the mitogenome, and this would penalize sequencing depth at the ends of the sequence. I suppose I could map twice, with two different breakpoints, but this seems like a severe waste of computational resources (I have hundreds of Gb of sequencing data to map). Does anyone know of a better way to accommodate circular genomes?