Abstract
Recent years have witnessed an increasing interest in the processing-in-memory (PIM) paradigm in computing due to its promise to improve the performance through the reduction of energy-hungry and long-latency memory accesses. Joined with the explosion of data to be processed, produced in genomics-particularly genome sequencing-PIM has become a potential promising candidate for accelerating genomics applications since they do not scale up well in conventional von Neumann systems. In this article, we present an in-memory accelerator architecture for DNA read alignment. This architecture outperforms corresponding software implementation by >49X and >18 000X, in terms of throughput and energy efficiency, respectively, even under conservative assumptions.
Original language | English (US) |
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Article number | 9064820 |
Pages (from-to) | 80-88 |
Number of pages | 9 |
Journal | IEEE Journal on Exploratory Solid-State Computational Devices and Circuits |
Volume | 6 |
Issue number | 1 |
DOIs | |
State | Published - Jun 2020 |
Bibliographical note
Publisher Copyright:© 2014 IEEE.
Keywords
- Accelerator
- Arrays
- BWA
- Bioinformatics
- Computational RAM
- DNA
- Genome Sequence
- Genomics
- Indexes
- Memory management
- Processing In Memory
- SHE-MTJ
- Sequential analysis