On Hardware-Accelerated Maximally-Efficient Systolic Arrays: Acceleration and Optimization of Genomics Pipelines Through Hardware/Software Co-Design

Developments in sequencing technology have drastically reduced the cost of DNA sequencing. The raw sequencing data being generated requires processing through computationally demanding suites of bioinformatics algorithms called genomics pipelines. The greatly decreased cost of sequencing has resulted in its widespread adoption, and the amount of...

Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths

We present our work on hardware accelerated genomics pipelines, using either FPGAs or GPUs to accelerate execution of BWA-MEM, a widely-used algorithm for genomic short read mapping. The mapping stage can take up to 40% of overall processing time for genomics pipelines. Our implementation offloads the Seed Extension function, one of the main...