Figure 2

GapFiller extension phase (an example with L = 5, Δ = 4, δ = 2, m = 2, T ₁ = 0.3, T ₂ = 0.5). (a) The putative overlapping reads, selected by their fingerprint values, are checked for the presence of mismatches and possibly discarded. For each remaining read (say, r₁, r₂, r₃, and r₄), the number of mismatches (highlighted in red) with S _i 's suffix does not exceed δ = 2. (b) The consensus string is computed for every position j such that either j ≤ F (C) or at least m = 2 reads are available. The characters rounded in gray and red refer to low-represented and non-represented positions, respectively. In presence of ambiguities (i.e., positions in which more than one character with the same representation rate occur) GapFiller chooses the character belonging to the first read encountered, from left to right. (c) Reads with mismatches in correspondence of the low-represented positions are discarded (say, r₁ and r₂), hence they do not contribute to reach the threshold m to compute a new consensus string. In our example read r₄'s tail is cut in the non-represented position, regardless on whether it matches the consensus string or not. (d) The reads still alive after Step 3 are used to compute the final consensus string C _new . Since there are 2 ≥ m available reads exceeding S _i 's tail, C _new is computed, it is attached to S _i , and the extended contig S_i+1is obtained.