PIM-Assembler: A processing-in-memory platform for genome assembly

Shaahin Angizi, Naima Ahmed Fahmi, Wei Zhang, Deliang Fan

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

In this paper, for the first time, we propose a high-throughput and energy-efficient Processing-in-DRAM-accelerated genome assembler called PIM-Assembler based on an optimized and hardware-friendly genome assembly algorithm. PIM-Assembler can assemble large-scale DNA sequence dataset from all-pair overlaps. We first develop PIM-Assembler platform that harnesses DRAM as computational memory and transforms it to a fundamental processing unit for genome assembly. PIM-Assembler can perform efficient X(N)OR-based operations inside DRAM incurring low cost on top of commodity DRAM designs (~5% of chip area). PIM-Assembler is then optimized through a correlated data partitioning and mapping methodology that allows local storage and processing of DNA short reads to fully exploit the genome assembly algorithm-level's parallelism. The simulation results show that PIM-Assembler achieves on average 8.4× and 2.3 wise× higher throughput for performing bulk bit-XNOR-based comparison operations compared with CPU and recent processing-in-DRAM platforms, respectively. As for comparison/addition-extensive genome assembly application, it reduces the execution time and power by ~5× and ~ 7.5× compared to GPU.

Original languageEnglish (US)
Title of host publication2020 57th ACM/IEEE Design Automation Conference, DAC 2020
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781450367257
DOIs
StatePublished - Jul 2020
Event57th ACM/IEEE Design Automation Conference, DAC 2020 - Virtual, San Francisco, United States
Duration: Jul 20 2020Jul 24 2020

Publication series

NameProceedings - Design Automation Conference
Volume2020-July
ISSN (Print)0738-100X

Conference

Conference57th ACM/IEEE Design Automation Conference, DAC 2020
CountryUnited States
CityVirtual, San Francisco
Period7/20/207/24/20

ASJC Scopus subject areas

  • Computer Science Applications
  • Control and Systems Engineering
  • Electrical and Electronic Engineering
  • Modeling and Simulation

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