FiltPIM: In-Memory Filter for DNA Sequencing

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.

Published in 2021 28th IEEE International Conference on Electronics, Circuits, and Systems (ICECS)

Cited by in corpus (2)

• BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis
• On Error Correction for Nonvolatile Processing-In-Memory