Figure 1

Graph Transformations. Each transformation modifies the genome graph such that the set of sequences consistent with the graph is unchanged. The nodes duplicated or removed by the simplification are shown as hollow circles. (a) Standard path compression collapses adjacent nodes u and v if v must follow u and u must precede v. (b) Portions of the cycle graph that are trees (shown as lines connecting square nodes) represent sections of the genome graph with a single solution. These can be collapsed into a single node connected to the rest of the sequence graph H. (c) Forward and backward half-decision nodes (those with either a single predecessor or a single successor) can be split into several nodes, which can usually be eliminated with path compression. (d) We can infer a path between a predecessor and successor if reasoning akin to the pigeonhole principle implies that at some point that predecessor must immediately precede that successor. (e) Some non-decision nodes u cannot be eliminated via path compression because both their predecessor and successors are decision nodes. In these cases, we can eliminate the non-decision node, and several edges, by replacing u with edges labeled with the sequence represented by u.