Search Results for author: Marquita Ellis

Found 2 papers, 2 papers with code

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly

3 code implementations • 20 Oct 2020 • Giulia Guidi, Oguz Selvitopi, Marquita Ellis, Leonid Oliker, Katherine Yelick, Aydin Buluc

In this work, we introduce new distributed-memory parallel algorithms for overlap detection and layout simplification steps of de novo genome assembly, and implement them in the diBELLA 2D pipeline.

Distributed, Parallel, and Cluster Computing Genomics

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LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

1 code implementation • 12 Feb 2020 • Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio, Steven Hofmeyr, Aydın Buluç, Leonid Oliker, Katherine Yelick

To highlight the impact of our work on a real-world application, we couple LOGAN with a many-to-many long-read alignment software called BELLA, and demonstrate that our implementation improves the overall BELLA runtime by up to 10. 6x.

Vocal Bursts Intensity Prediction

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Code

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