High-throughput Pairwise Alignment with the Wavefront Algorithm using Processing-in-Memory

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Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu, Izzat El Hajj

Published: 2022, Last Modified: 06 Aug 2024IPDPS Workshops 2022EveryoneRevisionsBibTeXCC BY-SA 4.0
Abstract: We show that the wavefront algorithm can achieve higher pairwise read alignment throughput on a UPMEM PIM system than on a server-grade multi-threaded CPU system.