Fig. 4

Scaffolding. a AGOUTI first builds an edge-weighted adjacency graph made up of contigs (vertices; black lines) and the joining-pairs between them (edges; purple arrows). Edges are weighted by the number of supporting joining-pairs. The graph is further simplified by removing edges with weight less than a user-specified value, and denoised using constraints described in the text and shown in Figs. 2 and 3. AGOUTI starts from leaf nodes (green vertices) and follows the highest-weighted edges. Each walk gives a scaffolding path, where the shortest such path has only two contigs. b Subgraphs with only non-leaf nodes that are ignored by RNAPATH. AGOUTI tries to traverse the subgraph starting from different vertices (shown in green). It records all the possible orders, each of which will be reconciled using constituent gene models to find the optimal one