HINGE: long-read assembly achieves optimal repeat resolution

The Contagion algorithm. (A) Two unbridged repeats are shown as orange segments. (B) The Contagion algorithm first kills the start-repeat annotation at u₂ (due to its overlap with u₁) and the end-repeat annotation at v₂ (due to its overlap with v₁). (C) The Contagion algorithm then kills the start-repeat annotation on u₃ (due to its internal match with u₁) and the end-repeat annotation on v₁ (due to its internal match with v₃). (D) Finally, an in-hinge is placed on u₁ and an out-hinge is placed on v₃. During the hinge-aided greedy assembly step, hinges allow u₂ and u₃ to choose the in-hinge at u₁ as their successor. Similarly, v₁ and v₂ pick the match starting at the out-hinge on v₃ as their predecessor match.