Abstract
Advances in DNA-sequencing technology have far
outpaced Moore’s law, imposing significant challenges on the
computationally intensive secondary analysis in the sequencing
pipeline. An accelerator for seed extension, a critical and com-
putationally intensive step in genome sequencing, is proposed.
The accelerator, implementing a string-independent automata,
consists of a triangular array of 25×2 custom-designed processing
elements. It performs 2.46 million reads per second (MRPS),
achieving a 158