A 2.46M reads/s Genome Sequencing Accelerator using a 625 Processing-Element Array

We present an accelerator for seed-extension, a critical and computational intensive step in genome sequencing. The accelerator consists of a triangular array of 25×25 custom design processing elements implementing a string-independent automata. It achieves 2.46M reads/s, a ~1800x performance improvement, and 27x smaller silicon footprint compared to a Xeon E5420.