Fig. 1.

Entities in the bidirected sequence graph. Top: a variation graph showing nodes (yellow rectangles), each of which contain a forward and reverse strand (red solid and dashed rectangles, respectively). Strands show the node identifier, the direction (+ or –) and the sequence of the strand. Note that reverse strands show the reverse complement sequence of the forward strand. All edges are shown as connections between nodes, with forward-to-forward edges denoted by solid lines, and reverse-to-reverse edges denoted by dashed lines. Two edges that invert from forward to reverse and reverse to forward are shown with dotted lines. Edges run from the strand at their beginning to that at their end, as indicated by the arrowhead. Bottom: an illustration of four paths. Each has a name, and can be referenced by a handle, which are omitted for brevity. Each path is shown in its natural direction as a series of connected steps that refer to strands in the graph. The first two paths differ by a SNP, with one passing through 2+:T, and the other through 3+:G. The third path is the reverse complement of the first. The fourth is the same as the first, but contains an inversion, passing through 5-:AATC rather than 5+:GATT. (Color version of this figure is available at Bioinformatics online.)