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 develops parsimonious and maximum likelihood models for assembling viral quasispecies and estimating their frequencies from 454 sequencing data. Our tools have been applied to several RNA viruses (HCV, HIV, IBV) as well as DNA viruses (HBV), genotyped using 454 Life Sciences amplicon and shotgun methods.

Committee
Dr. Alex Zelikovsky (chair)
Dr. Robert Harrison
Dr. Raj Sunderraman
Dr. Yury Khudyakov