2.4 Chromosome assembly using Hi-C
The Hi-C sequence data were aligned against the draft genome using JUICER v1.6.2 (https://github.com/aidenlab/juicer) (Durand et al., 2016). The uniquely mapped sequences were analyzed using 3D-DNA software (https://github.com/theaidenlab/3d-dna) to assist genomic assembly (Dudchenko et al., 2017). The algorithms “misjoin” and “scaffolding” were used to remove the misjoins and obtain scaffolds at the chromosomal level. The algorithm “seal” was employed to find the scaffolds that had been incorrectly removed by the “misjoin”. A heatmap of chromosome interactions was constructed to visualize the contact intensity among chromosomes using JUICER v1.6.2.