Edge criteria. For an overlap to become an edge in the overlap graph, it must satisfy three criteria. First, the overlap length l must be at least the minimal overlap length L. Second, the overlap quality score QS(R₁, R₂) must be at least the minimal score δ. For overlaps involving paired-end reads, we require both l₁ ≥ L and l₂ ≥ L, and, analogously, $QS(R_{1_a},R_{2_a})\ge \delta$ and $QS(R_{1_b},R_{2_b})\ge \delta$. Finally, we only accept overlaps where the sequence orientations of a paired-end read agree: either both sequences in forward orientation, or both sequences in reverse orientation.