Long read comparison

Context

Sequence alignment is an ubiquitous task in genomics analysis whose performance can be affected by the memory-wall on a processor-centric architecture. Processing-in-Memory (PiM) architectures provide a memory system with integrated computing capabilities to alleviate this bottleneck. We developed a long read optimised version of the Needleman and Wunsch algorithm for UPMEM PiM devices. On a server equipped with 20 UPMEM PiMs, this implementation outperforms standard alignment tools by an order of magnitude compared to a traditional multicore server.

Code link

https://github.com/upmem/usecase_dpu_alignment

Publications

M. Mognol, D. Lavenier, J. Legriel, Parallelization of the Banded Needleman & Wunsch Algorithm on UPMEM PiM Architecture for Long DNA Sequence Alignment. ICPP 2024: International Conference on Parallel Processing, Aug 2024, Gotland – Sweeden, France [hal]