2SNV: Quasispecies reconstruction from PacBio reads

Pacific Biosciences (PacBio) sequencing is providing thousands of reads with the length up to 10,000 bases. In most cases this length is enough to cover entire region of interest however this technology has high (≈15%) error rate. We propose a method for viral haplotype reconstruction using long SMRT reads. The proposed method based on correlation between SNVs and maximum likelihood for frequency estimation. When applied to PacBio reads from an Influenza A Virus (IAV) sample with ten variants, our method was able to reconstruct the nine most frequent.