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 journalArticle

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.

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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