Fig. 4

The cumulative assembly size (cdf) based on scaffolds for a different species in each row. The three rows represent analyses based on Chardonnay (a), mosquito (b) and thorny skate (c) data. There are two graphs for each species; the one on the left focuses on the chromosome length scaffold portion of the assembly (number of scaffolds), while the one on the right is the complete assembly on a log₁₀ (number of scaffolds) scale. Each graph for Chardonnay and mosquito have five lines and follow the key provided in the right-hand graph in panel B for mosquito. The analyses are scaffolded genome based on purge_dups (purge_dups + HiC), the unreduced assembly (-HapSolo −HC  +HiC), scaffold based on the HapSolo reduced assembly with BLAT preprocessing and without hill climbing (+HapSolo −HC  +HiC), and the scaffold based on the HapSolo reduced assembly with BLAT preprocessing and with hill climbing (+HapSolo +HC +HiC) and, finally, HapSolo reduced assembly with hill climbing using minimap2 (+HapSolo +MM2 +HC +HiC). In all graphs, the dotted line indicates the number of chromosomes for the species. c Reports results for thorny skate, which did not include BLAT processing. The HapSolo analyses are based on minimap2 alignments and presented with (+HC) and without (−HC) hillclimbing