A schematic diagram showing the DGA graph-based procedure. This diagram shows how to reconstruct allelic relationships and create the reference haploid assembly for a tiny diploid polymorphic assembly with eight scaffolds. The original diploid assembly (A), is first duplicated into two copies (B); then whole-genome pair-wise alignments are created between two assemblies (C). Based on the alignments, a DGA graph is created (D), from which a reduced linearized DGA graph is subsequently derived (E); guided by the reduced DGA graph, a reference haploid assembly can finally be created (F). This assembly has been included in the HaploMerger package as a simple example for testing. Readers may refer to Supplemental Figure S2 for more details regarding the conversion from the initial complicated DGA graph (D) into the reduced linearized DGA graph (E).
