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.

• This report represents the work of one or more WPI undergraduate students submitted to the faculty as evidence of completion of a degree requirement. WPI routinely publishes these reports on its website without editorial or peer review.

Creator

• Liu, Yilan

Publisher

• Worcester Polytechnic Institute

Identifier

• E-project-050514-125658

Advisor

• Wu, Zheyang

Year

• 2014

Date created

• 2014-05-05

Resource type

• Major Qualifying Project

Major

• Mathematical Sciences

Rights statement

• In Copyright