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

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

20222022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)18 citationsDOI

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.

Topics & Concepts

Computer scienceThroughputWavefrontPairwise comparisonAlgorithmParallel computingArtificial intelligenceOpticsPhysicsTelecommunicationsWirelessNeural Networks and Reservoir ComputingAdvanced Image and Video Retrieval TechniquesBlind Source Separation Techniques
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