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.
@article{arxiv.2205.15140,
title = {FiltPIM: In-Memory Filter for DNA Sequencing},
author = {Marcel Khalifa and Rotem Ben-Hur and Ronny Ronen and Orian Leitersdorf and Leonid Yavits and Shahar Kvatinsky},
journal= {arXiv preprint arXiv:2205.15140},
year = {2022}
}
Comments
Published in 2021 28th IEEE International Conference on Electronics, Circuits, and Systems (ICECS)