Profile-Driven Banded Smith-Waterman acceleration for Short Read Alignment

Short read alignment is a critical step in genomic pipelines that requires optimization due to the enormous input size and complexity of SmithWaterman string matching. Several optimization techniques have been examined, such as hardware acceleration, heuristics and pre-filtering. This work combines these approaches into a single powerful solution that leverages the low edit rate of reads and the principles of Banded SmithWaterman, to highlight the value of creating accelerators customized to the input accuracy requirements. We propose a dataset-specific multi-dataflow design that leverages both pre-filtering and Banded SmithWaterman to meet the demands of the datasets in both throughput and accuracy.