RASSA: Resistive Prealignment Accelerator for Approximate DNA Long Read Mapping

Abstract

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.