Poster: ViSpA: Viral spectrum assembling method

Like many RNA viruses, Hepatitis C virus (HCV) exists as a set of closely related sequences (quasispecies). The diversity of the quasispecies sequences can explain vaccines failures and virus resistance to existing therapies. Since the original software of next-generation sequencing systems assumes a single genome, there is a need for a new assembler that infers viral population in a host. Thus, the paper focuses on Quasispecies Spectrum Reconstruction (QSR) Problem: given a collection of 454 pyrosequencing reads taken from a sample quasispecies population, reconstruct the quasispecies spectrum, i.e., the set of sequences and the relative frequency of each sequence in the sample population.This poster introduces the ViSpA method that significantly extends previous approach by handling contaminated reads and overlaps with partial agreement between reads, by assembling haplotypes from per-vertex max-bandwidth paths via mutation-based clustering, and by estimating assemblies' frequencies via EM. A procedure to fix systematic 454 errors in homopolymers if they happen in the coding region is suggested.