Figure 3.

(A) Phasing pipeline. We called SNVs and partially phased them using the 10x Long Ranger pipeline. This generated haplotypes (partially phased blocks) with size distributions as shown below in (B). Heterozygous structural variants were called by aligning all PacBio reads to the hybrid assembly using NGMLR and Sniffles pipelines (Sedlazeck et al. 2018). Heterozygous SVs were then assigned to partial phased blocks using CrossStitch pipeline. Individual mitotic chromosomes were then sorted and sequenced to allow for assignment of haplotypes to homologs. (B) Partial phasing does not phase chromosomes completely. Here black triangles denote boundaries between partially phased blocks.