Classified as a complex big data analytics problem, DNA short read alignment serves as a major sequential bottleneck to massive amounts of data generated by next-generation sequencing platforms. With Von-Neumann computing architectures struggling to address such computationally-expensive and memory-intensive task today, Processing-in-Memory (PIM) platforms are gaining growing interests. In this paper, an energy-efficient and parallel PIM accelerator (AlignS) is proposed to execute DNA short read alignment based on an optimized and hardware-friendly alignment algorithm. We first develop AlignS platform that harnesses SOT-MRAM as computational memory and transforms it to a fundamental processing unit for short read alignment. Accordingly, we present a novel, customized, highly parallel read alignment algorithm that only seeks the proposed simple and parallel in-memory operations (i.e. comparisons and additions). AlignS is then optimized through a new correlated data partitioning and mapping methodology that allows local storage and processing of DNA sequence to fully exploit the algorithm-level's parallelism, and to accelerate both exact and inexact matches. The device-to-architecture co-simulation results show that AlignS improves the short read alignment throughput per Watt per mm(2) by similar to 12x compared to the ASIC accelerator. Compared to recent FM-index-based ReRAM platform, AlignS achieves 1.6x higher throughput per Watt.
