The complete pipeline of the Stitch algorithm by Shelton et al. (2015) (https://github.com/i5K-KINBRE-script-share/Irys-scaffolding/blob/master/KSU_bioinfo_lab/assemble_XeonPhi/assemble_XeonPhi_LAB.md) was run on the online cluster zythos provided by the Pawsey Supercomputing Center, Western Australia. The first draft genome assembly of T. subterraneum (TSUd_r1.1) (Hirakawa et al., 2016) was used as the reference genome. Super‐scaffolds were generated, and BioNano IrysView was used to examine the new assemblies and the alignments between BioNano consensus maps and the in silico scaffolds. Based on these alignments, misassemblies were identified in TSUd_r1.1 (Figure 1b).