A binning tool to reconstruct viral haplotypes from assembled contigs

Jiao Chen; Jiayu Shang; Jianrong Wang; Yanni Sun

Given the sequenced viral quasispecies, different types of analysis can be conducted to probe the genetic diversity. A relatively straightforward analysis is to understand the local diversity of known viruses by performing read mapping against reference genomes. While this type of analysis can produce a collection of local changes (mutations, insertions, or deletions) of the strains inside the quasispecies, it is not sufficient to infer the biological properties of the strains, which are more likely to be determined by multiple genes. In particular, epistatic interactions are abundant in RNA viruses, where the mutation of one gene masks the phenotypic effects of a mutation at another locus. Thus genome-scale reconstruction of the strains is essential for phenotype prediction of viruses .