Algorithmic details. (A) Read orientations: Given an edge u→v with orientations (−,+). Then, if u is labeled +, the induced label for v is −, while if u is labeled −, the induced label for v is +. This procedure leads to a vertex labeling in O(V) time. (B) Transitive edges: An edge u→w is called nontransitive, shown in black, if there is no vertex v such that there are edges u→v, v→w. It is called single transitive, shown in green, if for all vertices v such that there are edges u→v, v→w, one of the edges is nontransitive. It is called double transitive, shown in red, if there is a vertex v with edges u→v, v→w which are both transitive. (C) Read clustering by cliques (top) or by pairs (bottom). (D) Error correction: When a consensus sequence is constructed from a cluster of reads, the extremities are removed.