2.7 | Evaluation of genome assembly
Contiguity, misassemblies, and other assembly statistics were evaluated using Quast, which provides the maximum amount of information regarding assemblies (Gurevich, Saveliev, Vyahhi, & Tesler, 2013). Completeness of the assemblies was measured by searching for 3,354 vertebrate orthologs in a set of protein predictions generated by Augustus, as implemented in BUSCO (Simão, Waterhouse, Ioannidis, Kriventseva, & Zdobnov, 2015). Consistent regions between the resulting genome assembly and the “real” genome sequence, the best assembly based on experimental mate pairs or third-generation long reads, were identified using Mummer4 (Marçais et al., 2018) and then synteny between these were visualized using R (https://www.r-project.org/).