TY - GEN
T1 - Exploring DNA alignment-in-memory leveraging emerging sot-mRAM
AU - Angizi, Shaahin
AU - Zhang, Wei
AU - Fan, Deliang
N1 - Funding Information:
This work is supported in part by the National Science Foundation under Grant No.2005209, No.2003749, No. 1755761 and Semiconductor Research Corporation nCORE.
Publisher Copyright:
© 2020 Association for Computing Machinery.
PY - 2020/9/7
Y1 - 2020/9/7
N2 - 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.
AB - 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.
KW - Bioinformatics
KW - DNA Alignment
KW - Processing-in-Memory
UR - http://www.scopus.com/inward/record.url?scp=85091302487&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85091302487&partnerID=8YFLogxK
U2 - 10.1145/3386263.3407590
DO - 10.1145/3386263.3407590
M3 - Conference contribution
AN - SCOPUS:85091302487
T3 - Proceedings of the ACM Great Lakes Symposium on VLSI, GLSVLSI
SP - 277
EP - 282
BT - GLSVLSI 2020 - Proceedings of the 2020 Great Lakes Symposium on VLSI
PB - Association for Computing Machinery
T2 - 30th Great Lakes Symposium on VLSI, GLSVLSI 2020
Y2 - 7 September 2020 through 9 September 2020
ER -