Characterization of SVs using assembled whole-genomes and genome graphs using multiple reference genomes: (a) Schematic of structural variant (SV) discovery using alignment of assembled whole genomes. (b) Schematic of genome graphs, which can then be used to characterize a pangenome and facilitate rapid genotyping of individuals, as ‘core’ regions (genomic regions that do not vary among individuals) are readily distinguished from ‘accessory’ regions (genomic regions that do vary among individuals). Genome graphs can also facilitate accurate genotyping as more than one allele may be considered at once. The use of multiple reference genomes can reduce reference bias and are better able to capture insertions, inversion haplotypes and complex SVs (i.e., genomic regions where multiple SVs occur in close proximity).