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

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

Electrical and Computer Engineering

Research output: Contribution to journal › Article

Abstract

Recent years have witnessed an increasing interest in processing-in-memory paradigm in computing, owing to it’s promise to improve the performance through reduction of energy hungry and long latency memory accesses. Joined with explosion of data to be processed, produced in genomics – particularly genome sequencing, processing-in-memory has become a promising candidate for accelerating genomics applications since they do not scale up well in conventional Von-Neumann systems. In this paper, we present an in-memory accelerator architecture for DNA read alignment. This architecture outperforms corresponding software implementation by >49X and >18000X, in terms of throughput and energy efficiency respectively, even under conservative assumptions.

Original language	English (US)
Journal	IEEE Journal on Exploratory Solid-State Computational Devices and Circuits
DOIs	https://doi.org/10.1109/JXCDC.2020.2987527
State	Accepted/In press - Jan 1 2020

Keywords

Accelerator
Arrays
BWA
Bioinformatics
Computational RAM
DNA
Genome Sequence
Genomics
Indexes
Memory management
Processing In Memory
SHE-MTJ
Sequential analysis

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10.1109/JXCDC.2020.2987527

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Chowdhury, Z. I., Zabihi, M., Khatamifard, S. K., Zhao, Z., Resch, S., Razaviyayn, M., Wang, J. P., Sapatnekar, S. S., & Karpuzcu, U. R. (Accepted/In press). A DNA Read Alignment Accelerator based on Computational RAM. IEEE Journal on Exploratory Solid-State Computational Devices and Circuits. https://doi.org/10.1109/JXCDC.2020.2987527

A DNA Read Alignment Accelerator based on Computational RAM. / Chowdhury, Zamshed I.; Zabihi, Masoud; Khatamifard, S. Karen; Zhao, Zhengyang; Resch, Salonik; Razaviyayn, Meisam; Wang, Jian Ping ; Sapatnekar, Sachin S.; Karpuzcu, Ulya R.

In: IEEE Journal on Exploratory Solid-State Computational Devices and Circuits, 01.01.2020.

Research output: Contribution to journal › Article

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