PSI-RA: A parallel sparse index for read alignment on genomes

We concentrate on indexing DNA sequences via sparse suffix arrays (SSAs) and propose a new short read aligner named PSI-RA (parallel sparse index read aligner). The motivation in using SSAs is the ability to trade memory against time. It is possible to tune the space consumption of the index based on the available memory of the machine and the minimum length of the arriving pattern queries. Although SSAs have been studied before on exact matching of short reads, an elegant way of approximate matching capability was missing. We provide this by defining the right-most mismatch criteria that prioritizes the errors towards the end of the reads since it is known that the errors are more probable at that area. PSI-RA supports any number of mismatches in aligning reads. We give comparisons with some of the well known short read aligners, and show that indexing genome with SSA is a good alternative to Burrows-Wheeler transform or seed based solutions.