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GTC On-Demand

Bioinformatics & Genomics
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Implementing Modern Short Read DNA Alignment Algorithms in CUDA
Jonathan Cohen (NVIDIA)
Because of their inherently parallel and high-throughput nature, NVIDIA GPUs are a natural fit for the types of data-intensive computing required in bioinformatics applications. For many genomics applications, the primary challenge is to map hig ...Read More

Because of their inherently parallel and high-throughput nature, NVIDIA GPUs are a natural fit for the types of data-intensive computing required in bioinformatics applications. For many genomics applications, the primary challenge is to map highly divergent and control flow-heavy code to a SIMD architecture. By transforming complex serial flow of control into a sequence of communicating sequential processors running in parallel, we are able to achieve high throughput on very branchy code, while maintaining memory coherence and avoiding execution divergence. I will present initial results from NVIDIA''s internal "nvbio" project to develop efficient computational building blocks for analysis of Next-Generation Sequencing data, with a focus on implementations of BWA and Bowtie2-type aligners.

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Bioinformatics & Genomics, GTC 2013 - ID S3580
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