Date of Award
Summer 8-12-2013
Degree Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Computer Science
First Advisor
Alexander Zelikovsky
Second Advisor
Yury Khudyakov
Third Advisor
Robert Harrison
Fourth Advisor
Rajshekhar Sunderraman
Abstract
The genomic diversity of viral quasispecies is a subject of great interest, especially for chronic infections. Characterization of viral diversity can be addressed by high-throughput sequencing technology (454 Life Sciences, Illumina, SOLiD, Ion Torrent, etc.). Standard assembly software was originally designed for single genome assembly and cannot be used to assemble and estimate the frequency of closely related quasispecies sequences.
This work focuses on parsimonious and maximum likelihood models for assembling viral quasispecies and estimating their frequencies from 454 sequencing data. Our methods have been applied to several RNA viruses (HCV, IBV) as well as DNA viruses (HBV), genotyped using 454 Life Sciences amplicon and shotgun methods.
DOI
https://doi.org/10.57709/4313753
Recommended Citation
Tork, Bassam A., "Viral Quasispecies Reconstruction Using Next Generation Sequencing Reads." Dissertation, Georgia State University, 2013.
doi: https://doi.org/10.57709/4313753