July 8, 2019  |  

RASSA: Resistive Pre-Alignment Accelerator for Approximate DNA Long Read Mapping

Authors: Kaplan, Roman and Yavits, Leonid and Ginosar, Ran

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 pre-alignment outperforms the state-of-art solution, minimap2, by 16-77× with comparable accuracy and provides two orders of magnitude higher throughput than GateKeeper, a short-read pre-alignment hardware architecture implemented in FPGA.

Journal: IEEE Micro
DOI: 10.1109/MM.2018.2890253
Year: 2018

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