Figure 1.
An example of an acyclic pangenome graph built using three haplotypes. The left figure shows the optimal alignment of the query sequence to the DAG with minimum edit distance. Accordingly, the edit distance is zero, and the count of recombinations is two. Next, suppose that we use recombination penalty −5 (formally defined in Methods). The right figure shows the new optimal alignment, where there is no recombination because the alignment path is consistent with haplotype 2.
