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...

Computational Challenges of Next Generation Sequencing Pipelines Using Heterogeneous Systems

We are rapidly entering the era of genomics. The dramatic cost reduction of DNA sequencing due to the introduction of Next Generation Sequencing (NGS) techniques has resulted in an exponential growth of genetics data. The amount of data generated, and its associated processing into useful information, poses serious computational challenges. Here...