A framework for high-throughput sequence alignment using real processing-in-memory systems.

ABSTRACT:

Motivation

Sequence alignment is a memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory (PIM) architectures alleviate this bottleneck by providing the memory with computing competencies. We propose Alignment-in-Memory (AIM), a framework for high-throughput sequence alignment using PIM, and evaluate it on UPMEM, the first publicly available general-purpose programmable PIM system.

Results

Our evaluation shows that a real PIM system can substantially outperform server-grade multi-threaded CPU systems running at full-scale when performing sequence alignment for a variety of algorithms, read lengths, and edit distance thresholds. We hope that our findings inspire more work on creating and accelerating bi

SUBMITTER: Diab S 

PROVIDER: S-EPMC10159653 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature