A 2.46M Reads/s Seed-Extension Accelerator for Next-Generation Sequencing Using a String-Independent PE Array

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 computationally intensive step in genome sequencing, is proposed. The accelerator, implementing a string-independent automata, consists of a triangular array of $25\times 2$ custom-designed processing elements. It performs 2.46 million reads per second (MRPS), achieving a $1581\times $ improvement in power efficiency and $165.5\times $ smaller silicon footprint compared to a system setting with dual-socket Xeon E5-2697 v3 server processors.