FPGA Acceleration of Short Read Alignment

This work proposes a novel dataflow architecture for Smith-Waterman Matrix-fill and Traceback stages, which are at the heart of short- read alignment on NGS data. The FPGA accelerator is coupled with radical software restructuring to widely-used Bowtie2 aligner to deliver end-to-end speedup while preserving accuracy.

Speaker: Konstantina Koliogeorgi