Figure 5.

Breadcrumb algorithm. Two long contigs produced after error correction, A and B, are joined by several paired reads (red and blue arcs). The path between the two can be broken up because of a repeat internal to the connecting sequence, because of an overlap with a distinct part of the genome, or because of some unresolved errors. The small square nodes represent either nodes of the path between A and B, or other nodes of the graph connected to the former. Finding the exact path in the graph from A to B is not straightforward because of all the alternate paths that need to be explored. However, if we mark all the nodes that are paired up to either A or B (with a blue circle), we can define a subgraph much simpler to explore. Ideally, only a linear path connects both nodes.