An OðmlogmÞ OðmlogmÞ-Time Algorithm for Detecting Superbubbles

In genome assembly graphs, motifs such as tips, bubbles, and cross links are studied in order to find sequencing errors and to understand the nature of the genome. Superbubble, a complex generalization of bubbles, was recently proposed as an important subgraph class for analyzing assembly graphs. At present, a quadratic time algorithm is known. This paper gives an OðmlogmÞ-time algorithm to solve this problem for a graph with m edges.