A penalized regression approach to haplotype reconstruction of viral populations arising in early HIV/SIV infection.

ABSTRACT:

Motivation

Next generation sequencing (NGS) has been increasingly applied to characterize viral evolution during HIV and SIV infections. In particular, NGS datasets sampled during the initial months of infection are characterized by relatively low levels of diversity as well as convergent evolution at multiple loci dispersed across the viral genome. Consequently, fully characterizing viral evolution from NGS datasets requires haplotype reconstruction across large regions of the viral genome. Existing haplotype reconstruction algorithms have not been developed with the particular characteristics of early HIV/SIV infection in mind, raising the possibility that better performance could be achieved through a specifically designed algorithm.

Results

Here, we introduce a haplotype

SUBMITTER: Leviyang S 

PROVIDER: S-EPMC5870767 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature