One Reference Cannot Represent Everyone
A read spanning an insertion can be perfectly correct and still look broken against one linear genome. The mapper takes the blame for a reference that never contained the path.
pangraphmap creates a reference haplotype, an alternate structural-variant path, and reads that cross the bubble. Both mappers use the same mismatch rule; only the reference representation changes.
Add The Path, Remove The Bias
The linear mapper searches one string. The graph-aware mapper scores both valid haplotype paths and keeps the best alignment.
It is the smallest useful demonstration of why pangenomes matter: not because graphs are fashionable, but because missing variation turns into missing reads.
The Number
The linear reference maps 6 of 25 reads under the same edit threshold. The pangenome maps all 25, a 76-point gain.
This is a seeded structural-variant simulation, not a replacement for vg or Minigraph-Cactus. The benchmark and test run without third-party dependencies.
Research Basis
Inspired by Nature Genetics' 2025 pangenome graph review. The portfolio number above comes from this repository's own controlled benchmark, not from the paper.