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

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


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 languageEnglish (US)
Article number9064820
Pages (from-to)80-88
Number of pages9
JournalIEEE Journal on Exploratory Solid-State Computational Devices and Circuits
Issue number1
StatePublished - Jun 2020

Bibliographical note

Publisher Copyright:
© 2014 IEEE.


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


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