Accelerated Filtering and in situ Verification for Energy-Optimized Genome Read Mapping

Abstract

Whole genome sequencing (WGS) includes sequencing and assembly pipelines to extract biological genomes for new advances in healthcare, agriculture and environmental research. It produces small random sections of the genome, called reads, and then re-assembled by mapping those reads to a reference genome. This process called read mapping produces a large volume of data, which are disparately processed by compute- and memory-intensive filtering and verification algorithms. As such, the problem of energy-frugal read mapping has remained an open challenge. In this paper, we propose an accelerated read mapping methodology with combined filtering and verification, implemented on an FPGA platform. Core to our methodology is an algorithm based on q-gram lemma for filtration with Myers bit-vector for verification in tandem. Through in situ verification, the proposed implementation optimizes resource utilization between filtration and verification and introduces parallel pipelines in computation and storage processes. Our experimental analysis shows that this methodology gives up to 8.7× energy efficiency when implemented on the Zynq Ultrascale+ FPGA platform, compared with the state-of-the-art software and hardware approaches.