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.
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Chowdhury, Z. I., Zabihi, M., Khatamifard, S. K., Zhao, Z., Resch, S., Razaviyayn, M., … Karpuzcu, U. R. (2020). A DNA Read Alignment Accelerator Based on Computational RAM. IEEE Journal on Exploratory Solid-State Computational Devices and Circuits, 6(1), 80–88. https://doi.org/10.1109/JXCDC.2020.2987527
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