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GTC 2018 Silicon Valley

S8130 - Building a GPU-Accelerated Short-Read Aligner for Bisulfite-Treated DNA Sequences

Session Speakers
Session Description

It is not always easy to accelerate a complex serial algorithm with CUDA parallelization. A case in point is that of aligning bisulfite-treated DNA (bsDNA) sequences to a reference genome. A simple CUDA adaptation of a CPU-based implementation can improve the speed of this particular kind of sequence alignment, but it's possible to achieve order-of-magnitude improvements in throughput by organizing the implementation so as to ensure that the most compute-intensive parts of the algorithm execute on GPU threads.


Additional Information
Algorithms and Numerical Techniques, Genomics and Bioinformatics
Higher Education / Research, Healthcare & Life Sciences
Intermediate technical
Talk
25 minutes
Session Schedule