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GTC On-Demand

Bioinformatics & Genomics
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Introducing NVBIO: High Performance Primitives for Computational Genomics
Jonathan Cohen (NVIDIA), Nuno Subtil (NVIDIA)
Learn about NVIDIA's new open source CUDA/C++ library for high-performance computational genomics, NVBIO. NVBIO includes primitives for fast alignment using many variants of Smith-Waterman, text indexing via an FM-Index and related data structures, ...Read More
Learn about NVIDIA's new open source CUDA/C++ library for high-performance computational genomics, NVBIO. NVBIO includes primitives for fast alignment using many variants of Smith-Waterman, text indexing via an FM-Index and related data structures, and approximate string matching with backtracking. It also provides basic services like file IO and inter-thread communication. The design of NVBIO supports pipeline parallelism, where computation is expressed as a sequence of stages with queues to communicate between stages. Using this design concept, we have engineered an implementation of the Bowtie2 aligner on top of NVBIO, which aligns short read data 2-7x faster than the original Bowtie2 running on a high-end multicore CPU at comparable quality. In this talk we will introduce the codebase and demonstrate how to use it for your own applications.  Back
 
Keywords:
Bioinformatics & Genomics, GTC 2014 - ID S4741
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