A fast and efficient algorithm for mapping short sequences to a reference genome.

Novel high-throughput (Deep) sequencing technology methods have redefined the way genome sequencing is performed. They are able to produce tens of millions of short sequences (reads) in a single experiment and with a much lower cost than previous sequencing methods. In this paper, we present a new algorithm for addressing the problem of efficiently mapping millions of short reads to a reference genome. In particular, we define and solve the Massive Approximate Pattern Matching problem for mapping short sequences to a reference genome.