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...

Memory and Communication Profiling for Accelerator-Based Platforms

The growing demand of processing power is being satisfied mainly by an increase in the number of homogeneous and heterogeneous computing cores in a system. Efficient utilization of these architectures demands analysis of memory-access behaviour of applications and perform data-communication aware mapping of applications on these architectures....

An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm

We present the first accelerated implementation of BWA-MEM, a popular genome sequence alignment algorithm widely used in next generation sequencing genomics pipelines. The Smith-Waterman-like sequence alignment kernel requires a significant portion of overall execution time. We propose and evaluate a number of FPGA-based systolic array...