(a) In silico map of super‐scaffold 9 aligned to the BioNano optical maps (401× coverage). XMAP alignments for in silico map of sequence scaffolds 103, 143, 1029, 292 and 166 are shown. Consensus genome maps (blue with molecule map coverage shown in dark blue) align to the in silico maps of scaffolds (green with contigs overlaid as translucent coloured squares). An illustration of using BioNano optical maps to assist contig placement, scaffolding and inversion correction. Sequence scaffolds 103, 143, 1029, 292 and 166 were placed within super‐scaffold 9 by the optical maps and among these scaffolds; scaffolds 103, 143 and 166 were reversed in the super‐scaffold. (b) Illustration of misassemblies in the genome examined using BioNano optical maps. The super‐scaffold (colourful bar) contains scaffold Tsud_sc00127.10.1, scaffold Tsud_sc00415.00.1 and a gap between them. Compared with the optical map (blue bar), there are more Bsp QI restriction cut sites (displayed as straight lines) in the super‐scaffold at positions 2; there are some Bsp QI restriction cut sites missing at positions 1. At positions 3, 4 and 5, the super‐scaffold does not consist of BioNano consensus map. All those discordances can be examined in detail in the corresponding contigs or gaps (indicated above the super‐scaffold).