The neighbor-joining tree for the most frequent 10 candidate sequences obtained by ViSpA and ShoRAH (see Fig. 4 ) reminds a neighbor-joining tree for HCV quasispecies evolution. Additionally, the most frequent candidate sequence found by ViSpA is 99% identical to one of the actual ORFs obtained by cloning the quasispecies. 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." Figure 3 Percentage of candidate sequences which cumulative frequency is 85%, 90%, and 95%. The values on x-axis corresponds to the number of allowed mismatches during read graph construction. n_m means that up to n mismatches are allowed in superreads and up to m mismatches are allowed in edges.