Inferring viral quasispecies spectra from 454 pyrosequencing reads

BMC Bioinformatics

Table 1 Comparison of three methods – ViSpA, ShoRAH, and ShoRAHreads+ViSpA – on the read data simulated by FlowSim.

The quasispecies sequence is considered found if one of candidate sequences matches it exactly (k = 0) or with at most k (1 or 9) mismatches. All methods are run 100 times on 10% - reduced data. For the i-th (i = 1, .., 10) most frequent sequence assembled on the whole data, we record its reproducibility, i.e., percentage of runs when there is a match (exact or with at most k mismatches) among 10 most frequent sequences found on reduced data. ”Reproducibility: Max” and ”Reproducibility: Average” report respectively maximum and average of those percentages.”

ISSN: 1471-2105