RASSA: Resistive Prealignment Accelerator for Approximate DNA Long Read Mapping

Roman Kaplan, Leonid Yavits, Ran Ginosar

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive approximate similarity search accelerator (RASSA) exploits charge distribution and parallel in-memory processing to reflect a mismatch count between DNA sequences. RASSA implementation of DNA long-read prealignment outperforms the state-of-the-art solution, minimap2, by 16-77× with comparable accuracy and provides two orders of magnitude higher throughput than GateKeeper, a short-read prealignment hardware architecture implemented in FPGA.

Original languageEnglish
Article number8594624
Pages (from-to)44-54
Number of pages11
JournalIEEE Micro
Issue number4
StatePublished - 1 Jul 2019
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2018 IEEE.


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