DNA Pre-Alignment Filter Using Processing Near Racetrack Memory

Abstract

Recent DNA <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">pre-alignment</i> filter designs employ DRAM for storing the reference genome and its associated meta-data. However, DRAM incurs increasingly high energy consumption of background and refresh energy as devices scale. To overcome this problem, this paper explores a design with <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">racetrack memory</i> (RTM)–an emerging non-volatile memory that promises higher storage density, faster access latency, and lower energy consumption. Multi-bit storage cells in RTM are inherently sequential and thus require data placement strategies to mitigate the performance and energy impacts of shifting during data accesses. We propose a near-memory pre-alignment filter with a novel data mapping and several shift reduction strategies designed explicitly for RTM. On a set of four input genomes from the 1000 Genome Project, our approach improves performance and energy efficiency by 68% and 52%, respectively, compared to the state-of-the-art DRAM-based architecture.