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 16-77x with comparable accuracy and provides two orders of magnitude higher throughput than GateKeeper, a short-read pre-alignment hardware architecture implemented in FPGA.
@article{arxiv.1809.01127,
title = {RASSA: Resistive Pre-Alignment Accelerator for Approximate DNA Long Read Mapping},
author = {Roman Kaplan and Leonid Yavits and Ran Ginosar},
journal= {arXiv preprint arXiv:1809.01127},
year = {2019}
}