Figure 6.
The Poisoning algorithm. Read poisoning is part of the process by which we prevent a bridged repeat from collapsing on the graph. (A) In this scenario, read u1 is initially given a start-repeat annotation, which is killed in the Contagion algorithm, as the repeat is bridged by read w. In this case, we keep a poisoned annotation on read u1. (B) When v2 looks for its best predecessor, it skips u1 due to the poisoned repeat annotation, preventing a misassembly.
