CCGG

The Collaborative Cross Graphical Genome (CCGG) is a graph-based pangenome representation for the widely-used recombinant-inbred mouse genetic reference population known as the Collaborative Cross (CC). This version was constructed by merging the standard mouse reference, GRCm38, with de novo assemblies of the 7 founder's genomes guided by the short-read sequence data from CC-line samples. It packs 83 genomes in a single graph which directly captures important notions relating genomes such as identity-by-descent between mouse strains, and highly variable genomic regions. The introduction of special anchor nodes with sequence data provides a coordinate framework that divides all genomes into homologous segments. Parallel edges between anchors contain all genomic variants and indicate shared haplotypes. Furthermore, genomic annotations are provided that include gene and exon intervals, repeat types, and the of alignments edges relative to the mouse reference assembly. The graphical structure of the CCGG with annotations provides a comprehensive picture of the genome structure surrounding biological features, which are easy to traverse for searching, annotating, comparing and visualizing features. Integrating sequencing data with CCGG, the recombination hotspots, especially within the gene regions, are identified in CC strains. THe CCGG provides an effective pangenome model that represents the genetic diversity of the CC and facilitates tool chain development for downstream analysis.