TY - GEN
T1 - Enabling Highly-Efficient DNA Sequence Mapping via ReRAM-based TCAM
AU - Lai, Yu Shao
AU - Chen, Shuo Han
AU - Chang, Yuan Hao
N1 - Publisher Copyright:
© 2023 IEEE.
PY - 2023
Y1 - 2023
N2 - In the post-pandemic era, third-generation DNA sequencing (TGS) has received increasing attention from both academics and industries. As TGS technologies have become a requisite for extracting DNA sequences, the DNA sequence mapping, which is the most basic bioinformatics application and the core of polymerase chain reaction (PCR) tests, receives great challenges, due to the large size and noisy nature of TGS technologies. In addition, the ever-increasing data volume of DNA sequences also induces the issue of memory wall while large datasets are moved between the memory and the computing units. However, much less effort has been devoted to DNA sequence mapping acceleration while considering both the memory wall issue and the challenges of TGS technologies. To enable highly-efficient DNA sequence mapping, this study proposes a novel resistive random-access memory (ReRAM)-based ternary content-addressable memory (TCAM) and exploits the intrinsic parallelity of ReRAM crossbar for efficient mapping acceleration. Promising results have been demonstrated through a series of experiments with different scales of datasets.
AB - In the post-pandemic era, third-generation DNA sequencing (TGS) has received increasing attention from both academics and industries. As TGS technologies have become a requisite for extracting DNA sequences, the DNA sequence mapping, which is the most basic bioinformatics application and the core of polymerase chain reaction (PCR) tests, receives great challenges, due to the large size and noisy nature of TGS technologies. In addition, the ever-increasing data volume of DNA sequences also induces the issue of memory wall while large datasets are moved between the memory and the computing units. However, much less effort has been devoted to DNA sequence mapping acceleration while considering both the memory wall issue and the challenges of TGS technologies. To enable highly-efficient DNA sequence mapping, this study proposes a novel resistive random-access memory (ReRAM)-based ternary content-addressable memory (TCAM) and exploits the intrinsic parallelity of ReRAM crossbar for efficient mapping acceleration. Promising results have been demonstrated through a series of experiments with different scales of datasets.
KW - DNA
KW - ReRAM
KW - sequence mapping
KW - TCAM
UR - http://www.scopus.com/inward/record.url?scp=85173076287&partnerID=8YFLogxK
U2 - 10.1109/ISLPED58423.2023.10244730
DO - 10.1109/ISLPED58423.2023.10244730
M3 - Conference contribution
AN - SCOPUS:85173076287
T3 - Proceedings of the International Symposium on Low Power Electronics and Design
BT - 2023 IEEE/ACM International Symposium on Low Power Electronics and Design, ISLPED 2023
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - 2023 IEEE/ACM International Symposium on Low Power Electronics and Design, ISLPED 2023
Y2 - 7 August 2023 through 8 August 2023
ER -