Fig. 3

Time complexity, feasibility, and correctness of PhaseDancer. A Computational time performance (y-axis) for different number of stacked SDs (x-axis) and processes (colour scale). Each boxplot represents 100 iterations of PhaseDancer for a given setting. B Feasibility space for SDs in human. PhaseDancer resolves all SDs with the number of stacked SDs per base as for SDs identified by T2T human genome assembly (area plot, Fig. 2C). For a given number of stacked SDs (x-axis) the height of each bar indicates an average runtime of PhaseDancer iteration (right y-axis) along with a standard deviation (error bars) and individual measurements (points). C The evaluation of PhaseDancer assemblies using the Phred Quality Score (Q; y-axis). The samples used for evaluation were generated by PhaseDancerSimulator, with fixed parameters including a coverage of 40x, an average read length of 18 kb, and a read length standard deviation of 3 kb. The x-axis represents different sequencing error levels, while the colour scale indicates different numbers of cis-morphisms per 10 kb window. The additional upper panel in the figure shows the percentage of assembly tasks with no errors (Q > 60) using bar plots. Remarkably, our analyses revealed no significant changes in assembly quality for different PhaseDancerSimulator topologies (SDs evolutionary scenarios). D Correctness of the PhaseDancer assemblies was assessed using optical genome mapping (OGM). All HSA2 syntenic sites of the chimpanzee genome were in concordance with the corresponding OGM molecules (BssSI enzyme shown)