Figure 1.
An assembly 'bubble'. An assembly 'bubble' that complicates repeat resolution with mate-pairs. Shaded nodes are non-decision nodes (in- and out-degree equal to 1). The nodes R1 and R2 are decision nodes (repeats). There are two possible paths of the same length from one end of the mate-pair to the other (black nodes), leading to ambiguity in the graph traversal.
