Fig. 3

Merqury set operations for generating haplotype-specific hap-mers and reliable k-mers. a Venn diagram of maternal, paternal, and child k-mer sets. Inherited haplotype-specific k-mers (hap-mers) are estimated from the parental and child k-mer sets. Roughly half of the parental-specific k-mers are inherited by a child. b Set operation examples used in Meryl to compute hap-mers and other k-mer sets. c, d Stacked k-mer multiplicity of the child’s read set, colored by inheritance. K-mers are colored by maternal (red) paternal (blue) and shared between parents (green). K-mers only seen in the child’s reads (black) are mostly from low-copy sequencing errors or k-mers arising from de novo variants in the child. Reliable k-mer thresholds used for generating completeness scores for all k-mers (black) and hap-mers (red and blue) are marked by dashed lines