Fig. 2.

Benchmarking for P. polytes and B. japonicum. a Alignment between the P. polytes bubbles mapped to the dsx-gene locus. Dot plot was obtained using Nucmer and a modified version of Mummerplot in Mummer package⁵⁷. b Alignment between Platanus-allee bubble and the results obtained using other methods for the dsx-gene locus. c Precision-recall evaluation of B. japonicum based on Moleculo synthetic long reads. Underlined numbers indicate F-measures (harmonic mean of recall and precision). d Relation between phasing performances and heterozygosity of amphioxus. e Examples of highly divergent Platanus-allee bubbles obtained in the amphioxus analysis. Heterozygosities between bubble sequences were calculated based on the sequence difference (1 − (number of matches/alignment-length)) for the mapped 1k-mer pairs obtained from the Moleculo data using 100 kbp-windows. Alignments (“Arrangements of other results”) in b, e were performed using Minimap2²⁰ (see “Methods” section)