The Importance of Being X-Drop: High Performance Genome Alignment on Reconfigurable Hardware

Pairwise sequence alignment accounts for the majority of key genome analysis applications’ runtime. Because of the quadratic time complexity of exact alignment algorithms, the community is moving away from exact algorithms in favor of heuristics that only compute high-quality results. However, the state of the art lacks hardware-accelerated versions of these heuristic algorithms as the vast majori...