  The recent advances in sequencing technologies enables the assembly of
individual genomes to the reference quality. How to integrate multiple genomes
from the same species and to make the integrated representation accessible to
biologists remain an open challenge. Here we propose a graph-based data model
and associated formats to represent multiple genomes while preserving the
coordinate of the linear reference genome. We implemented our ideas in the
minigraph toolkit and demonstrate that we can efficiently construct a pangenome
graph and compactly encode tens of thousands of structural variants missing
from the current reference genome.
