Fig. 7.

Examples of assembly graph defects in . Given two nodes , an $s-t$ path is a path starting in s and ending in t. A simple bubble consists of two vertex disjoint $s-t$ paths. This construct can be extended to super-bubbles, defined as a set of $s-t$ paths, exactly including all nodes reachable from s without passing t and vice versa. Bubbles and superbubbles are primarily the result of unrecognized overlaps. Tips are “side branches” that do not reconnect with the dominating paths and thus have distinct end-points. Crosslinks, finally, are connecting edges between two golden paths