AligneR: A Process-in-Memory Architecture for Short Read Alignment in ReRAMs

Abstract

Genomics is the key to enable the personal customization of medical care. How to fast and energy-efficiently analyze the huge amounts of genomic sequence data generated by next generation sequencing technologies has become one of the most significant challenges facing genomics today. Existing hardware platforms achieve low genome sequencing throughput with significant hardware and power overhead. In this paper, we propose AligneR, a ReRAM-based process-in-memory architecture, to accelerate the bottleneck of genome sequencing, i.e., short read alignment. Compared to state-of-the-art accelerators, AligneR improves the short read alignment throughput per Watt per <inline-formula><tex-math notation="LaTeX">$mm^2$</tex-math></inline-formula> by <inline-formula><tex-math notation="LaTeX">$13\times$</tex-math></inline-formula> .