Exploring DNA alignment-in-memory leveraging emerging sot-mRAM

Shaahin Angizi, Wei Zhang, Deliang Fan

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

Abstract

In this work, we review two alternative Processing-in-Memory (PIM) accelerators based on Spin-Orbit-Torque Magnetic Random Access Memory (SOT-MRAM) to execute DNA short read alignment based on an optimized and hardware-friendly alignment algorithm. We first discuss the reconstruction of the existing sequence alignment algorithm based on BWT and FM-index such that it can be fully implemented leveraging PIM functions. We then transform SOT-MRAM array to a potential computational memory by presenting two different reconfigurable sense amplifiers to accelerate the reconstructed alignment-in-memory algorithm. The cross-layer simulation results show that such PIM platforms are able to achieve a nearly ten-fold and two-fold increases in throughput/power/area measure compared with recent ASIC and processing-in-ReRAM designs, respectively.

Original languageEnglish (US)
Title of host publicationGLSVLSI 2020 - Proceedings of the 2020 Great Lakes Symposium on VLSI
PublisherAssociation for Computing Machinery
Pages277-282
Number of pages6
ISBN (Electronic)9781450379441
DOIs
StatePublished - Sep 7 2020
Event30th Great Lakes Symposium on VLSI, GLSVLSI 2020 - Virtual, Online, China
Duration: Sep 7 2020Sep 9 2020

Publication series

NameProceedings of the ACM Great Lakes Symposium on VLSI, GLSVLSI

Conference

Conference30th Great Lakes Symposium on VLSI, GLSVLSI 2020
CountryChina
CityVirtual, Online
Period9/7/209/9/20

Keywords

  • Bioinformatics
  • DNA Alignment
  • Processing-in-Memory

ASJC Scopus subject areas

  • Engineering(all)

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