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arXiv · 2205.15140

FiltPIM: In-Memory Filter for DNA Sequencing

Marcel Khalifa·Rotem Ben-Hur·Ronny Ronen·Orian Leitersdorf·Leonid Yavits·Shahar Kvatinsky
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Abstract

Aligning the entire genome of an organism is a compute-intensive task. Pre-alignment filters substantially reduce computation complexity by filtering potential alignment locations. The base-count filter successfully removes over 68% of the potential locations through a histogram-based heuristic. This paper presents FiltPIM, an efficient design of the basecount filter that is based on memristive processing-in-memory. The in-memory design reduces CPU-to-memory data transfer and utilizes both intra-crossbar and inter-crossbar memristive stateful-logic parallelism. The reduction in data transfer and the efficient stateful-logic computation together improve filtering time by 100x compared to a CPU implementation of the filter.

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Marcel Khalifa, Rotem Ben-Hur, Ronny Ronen, Orian Leitersdorf, Leonid Yavits, Shahar Kvatinsky. 2022-05-30. FiltPIM: In-Memory Filter for DNA Sequencing. https://doi.org/10.1109/icecs53924.2021.9665570

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