Fig. 1

An illustration of co-linear chaining for sequence-to-graph alignment. Assume that the vertices of the graph are labeled with nucleotide sequences. In panel a, short exact matches, i.e., anchors, are illustrated using red blocks joined by dotted lines. In panel b, the anchors corresponding to the best-scoring chain are retained, and the rest are removed. The retained anchors are combined to produce an alignment of the query sequence to the graph (illustrated using a green curved line)