A DNA Read Alignment Accelerator Based on Computational RAM

Zamshed I. Chowdhury; Masoud Zabihi; S. Karen Khatamifard; Zhengyang Zhao; Salonik Resch; Meisam Razaviyayn; Jian-Ping Wang; Sachin S. Sapatnekar; Ulya R. Karpuzcu

doi:10.1109/JXCDC.2020.2987527

IEEE Journal on Exploratory Solid-State Computational Devices and Circuits (Jan 2020)

A DNA Read Alignment Accelerator Based on Computational RAM

Zamshed I. Chowdhury,
Masoud Zabihi,
S. Karen Khatamifard,
Zhengyang Zhao,
Salonik Resch,
Meisam Razaviyayn,
Jian-Ping Wang,
Sachin S. Sapatnekar,
Ulya R. Karpuzcu

Affiliations

Zamshed I. Chowdhury: ORCiD; Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
Masoud Zabihi: ORCiD; Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
S. Karen Khatamifard: ORCiD; Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
Zhengyang Zhao: ORCiD; Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
Salonik Resch: Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
Meisam Razaviyayn: University of Southern California, Los Angeles, CA, USA
Jian-Ping Wang: ORCiD; Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
Sachin S. Sapatnekar: ORCiD; Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
Ulya R. Karpuzcu: Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA

DOI: https://doi.org/10.1109/JXCDC.2020.2987527
Journal volume & issue: Vol. 6, no. 1
pp. 80 – 88

Abstract

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Recent years have witnessed an increasing interest in the processing-in-memory (PIM) paradigm in computing due to its promise to improve the performance through the reduction of energy-hungry and long-latency memory accesses. Joined with the explosion of data to be processed, produced in genomics - particularly genome sequencing - PIM has become a potential promising candidate for accelerating genomics applications since they do not scale up well in conventional von Neumann systems. In this article, we present an in-memory accelerator architecture for DNA read alignment. This architecture outperforms corresponding software implementation by >49X and >18 000X, in terms of throughput and energy efficiency, respectively, even under conservative assumptions.

Published in IEEE Journal on Exploratory Solid-State Computational Devices and Circuits

ISSN: 2329-9231 (Online)
Publisher: IEEE
Country of publisher: United States
LCC subjects: Technology: Electrical engineering. Electronics. Nuclear engineering: Electronics: Computer engineering. Computer hardware
Website: https://ieeexplore.ieee.org/xpl/RecentIssue.jsp?punumber=6570653

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