Award Date

December 2016

Degree Type

Thesis

Degree Name

Master of Science in Computer Science

Department

Computer Science

First Committee Member

Kazem Taghva

Second Committee Member

Ajoy Datta

Third Committee Member

Laxmi Gewali

Fourth Committee Member

Emma Regentova

Number of Pages

64

Abstract

In this thesis, we report on the use of minhash techniques to improve the draft assembly of a genome mapping. More specifically, we use minhash to compare the scaffolds of sea urchin and sea cucumber genomes.

One of the main contributions of this thesis is the implementation of minhash with the Message Passing Interface (MPI) utilizing Intel Phi co-processors. It is shown that our implementation significantly reduces the processing time for identification of k-mer similarities.

Keywords

data mining; data science; genome mapping; minhash; parallel programming; pattern recognition

Disciplines

Computer Sciences

Language

English


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