FiltPIM: In-Memory Filter for DNA Sequencing

Marcel Khalifa, Rotem Ben-Hur, Ronny Ronen, Orian Leitersdorf, Leonid Yavits, Shahar Kvatinsky

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

8 Scopus citations

Abstract

Aligning the entire genome of an organism is a compute-intensive task. Pre-alignment filters substantially reduce computation complexity by filtering potential alignment locations. The base-count filter successfully removes over 68% of the potential locations through a histogram-based heuristic. This paper presents FiltPIM, an efficient design of the base-count filter that is based on memristive processing-in-memory. The in-memory design reduces CPU-to-memory data transfer and utilizes both intra-crossbar and inter-crossbar memristive stateful-logic parallelism. The reduction in data transfer and the efficient stateful-logic computation together improve filtering time by 100x compared to a CPU implementation of the filter.

Original languageEnglish
Title of host publication2021 28th IEEE International Conference on Electronics, Circuits, and Systems, ICECS 2021 - Proceedings
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781728182810
DOIs
StatePublished - 2021
Externally publishedYes
Event28th IEEE International Conference on Electronics, Circuits, and Systems, ICECS 2021 - Dubai, United Arab Emirates
Duration: 28 Nov 20211 Dec 2021

Publication series

Name2021 28th IEEE International Conference on Electronics, Circuits, and Systems, ICECS 2021 - Proceedings

Conference

Conference28th IEEE International Conference on Electronics, Circuits, and Systems, ICECS 2021
Country/TerritoryUnited Arab Emirates
CityDubai
Period28/11/211/12/21

Bibliographical note

Publisher Copyright:
© 2021 IEEE.

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