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 › peer-review

2 Scopus citations

Abstract

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.

Original language	English (US)
Article number	9064820
Pages (from-to)	80-88
Number of pages	9
Journal	IEEE Journal on Exploratory Solid-State Computational Devices and Circuits
Volume	6
Issue number	1
DOIs	https://doi.org/10.1109/JXCDC.2020.2987527
State	Published - Jun 2020

Bibliographical note

Funding Information:
This work was supported in part by NSF under Grant SPX-1725420.

Publisher Copyright:
© 2014 IEEE.

Keywords

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

UN SDGs

This output contributes to the following Sustainable Development Goal(s)

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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, Vol. 6, No. 1, 9064820, 06.2020, p. 80-88.

Research output: Contribution to journal › Article › peer-review

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abstract = "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. ",

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note = "Funding Information: This work was supported in part by NSF under Grant SPX-1725420. Publisher Copyright: {\textcopyright} 2014 IEEE.",

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A DNA Read Alignment Accelerator Based on Computational RAM

Abstract

Bibliographical note

Keywords

UN SDGs

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