Fig. 2

The dikaryotic phasing pipeline for assigning contigs into the two haplotypes A and B. A gene binning method was developed to phase the assembly into the two haplotypes prior to scaffolding of each haplotype separately. Genes that map exactly twice to the unphased assembly were used to assign contigs into scaffold bins that represent the two haplotypes. Hi-C contacts within allelic scaffold bins were ignored and the bins were clustered into the two haplotypes with a graph approach. Phase switches within scaffold bins were visualized, manually corrected and steps 1 and 2 were run again. Finally, unplaced contigs are assigned to the haplotypes based on synteny and Hi-C contacts