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

From: Inferring viral quasispecies spectra from 454 pyrosequencing reads

  ShoRAH ViSpA ShoRAHreads+ViSpA
  PPV Sensitivity Reproducibility PPV Sensitivity Reproducibility PPV Sensitivity Reproducibility
    Max Average    Max Average    Max Average
k=0 0.0097 0.3 0.45 0.11 0.0008 0.1 0.1 0.1 0.5 0.5 0.95 0.95
k=1 0.0129 0.4 0.6 0.32 0.0008 0.1 0.1 0.1 0.5 0.5 0.95 0.95
k=9 0.0162 0.5 0.95 0.64 0.0015 0.2 0.1 0.1 0.5 1 0.95 0.95
  1. 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.”
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