Center for Computational Molecular Biology Seminar
"Inferring Viral Quasispecies Spectra from NGS Reads"
Ion Mandoiu, University of Connecticut, Dept. of Computer Science & Engineering
Wednesday, February 1, 2012 at 4:00 P.M.
Room 241 Swig Boardroom (2nd Floor CIT)
RNA viruses infecting a host usually exist as a set of closely related sequences, referred to as quasispecies. The genomic diversity of viral quasispecies infecting a host is of great interest, particularly for chronic infections, since it can lead to resistance to existing antiviral therapies. By eliminating time-consuming cloning steps and providing unprecedented sequencing depth, next-generation sequencing (NGS) technologies promise to enhance our ability to characterize quasispecies spectra of infected hosts. Unfortunately, standard assembly software was originally designed for haploid genome reconstruction, and cannot be used to simultaneously assemble and estimate the abundance of multiple closely related quasispecies sequences. In this talk I will present several algorithms for quasispecies spectrum reconstruction and frequency estimation from both shotgun and amplicon NGS reads. Results of empirical comparisons with existing methods on simulated and real 454 pyrosequencing reads will also be presented.