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...

Power-Efficiency Analysis of Accelerated BWA-MEM Implementations on Heterogeneous Computing Platforms

Next Generation Sequencing techniques have dramatically reduced the cost of sequencing genetic material, resulting in huge amounts of data being sequenced. The processing of this data poses huge challenges, both from a performance perspective, as well as from a power-efficiency perspective. Heterogeneous computing can help on both fronts, by...

An Efficient GPU-Accelerated Implementation of Genomic Short Read Mapping with BWA-MEM

Next Generation Sequencing techniques have resulted in an exponential growth in the generation of genetics data, the amount of which will soon rival, if not overtake, other Big Data elds, such as astronomy and streaming video services.<br/>To become useful, this data requires processing by a complex pipeline of algorithms, taking multiple days...

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...