AlignS: A processing-in-memory accelerator for DNA short read alignment leveraging SOT-MRAM

Shaahin Angizi, Jiao Sun, Wei Zhang, Deliang Fan

Research output: Chapter in Book/Report/Conference proceedingConference contribution

11 Scopus citations

Abstract

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 perWatt perm2 by ∼12× compared to the ASIC accelerator. Compared to recent FM-index-based ReRAM platform, AlignS achieves 1.6× higher throughput per Watt.

Original languageEnglish (US)
Title of host publicationProceedings of the 56th Annual Design Automation Conference 2019, DAC 2019
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781450367257
DOIs
StatePublished - Jun 2 2019
Externally publishedYes
Event56th Annual Design Automation Conference, DAC 2019 - Las Vegas, United States
Duration: Jun 2 2019Jun 6 2019

Publication series

NameProceedings - Design Automation Conference
ISSN (Print)0738-100X

Conference

Conference56th Annual Design Automation Conference, DAC 2019
CountryUnited States
CityLas Vegas
Period6/2/196/6/19

ASJC Scopus subject areas

  • Computer Science Applications
  • Control and Systems Engineering
  • Electrical and Electronic Engineering
  • Modeling and Simulation

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