@inproceedings{73fd78721c03433882cf88af81a638c1,
title = "Exploring DNA alignment-in-memory leveraging emerging sot-mRAM",
abstract = "In this work, we review two alternative Processing-in-Memory (PIM) accelerators based on Spin-Orbit-Torque Magnetic Random Access Memory (SOT-MRAM) to execute DNA short read alignment based on an optimized and hardware-friendly alignment algorithm. We first discuss the reconstruction of the existing sequence alignment algorithm based on BWT and FM-index such that it can be fully implemented leveraging PIM functions. We then transform SOT-MRAM array to a potential computational memory by presenting two different reconfigurable sense amplifiers to accelerate the reconstructed alignment-in-memory algorithm. The cross-layer simulation results show that such PIM platforms are able to achieve a nearly ten-fold and two-fold increases in throughput/power/area measure compared with recent ASIC and processing-in-ReRAM designs, respectively.",
keywords = "Bioinformatics, DNA Alignment, Processing-in-Memory",
author = "Shaahin Angizi and Wei Zhang and Deliang Fan",
note = "Publisher Copyright: {\textcopyright} 2020 Association for Computing Machinery.; 30th Great Lakes Symposium on VLSI, GLSVLSI 2020 ; Conference date: 07-09-2020 Through 09-09-2020",
year = "2020",
month = sep,
day = "7",
doi = "10.1145/3386263.3407590",
language = "English (US)",
series = "Proceedings of the ACM Great Lakes Symposium on VLSI, GLSVLSI",
publisher = "Association for Computing Machinery",
pages = "277--282",
booktitle = "GLSVLSI 2020 - Proceedings of the 2020 Great Lakes Symposium on VLSI",
}