In this project we develop Graphics Processing Unit (GPU) based tools to address the statistical computation challenges in analyzing the next-generation sequencing data. Our work contains three components. First, we accelerate general statistical analysis in R. After studying various approaches of using GPU in R, we adopted the best solution to combine R with GPU. Second, we address a set of specific computation-intensive problems in simulating genetic variants in whole-genome sequencing data. Third, we break the CPU limitation of Variant Tools, a popular toolkit for the next-gen sequencing analysis, by extending its functionality to more the powerful parallel computation of GPU.
Worcester Polytechnic Institute
Major Qualifying Project
All authors have granted to WPI a nonexclusive royalty-free license to distribute copies of the work, subject to other agreements. Copyright is held by the author or authors, with all rights reserved, unless otherwise noted.