2.4 Hi-C assembly of the chromosome-level genome
We constructed a Hi-C library using the Illumina NovaSeq platform. Bowtie2-2.2.5 (Langmead and Salzberg, 2012) was used to align the raw reads to the assembled contigs, and then we filtered low quality reads using a HiC-Pro pipeline (Servant et al., 2015) with the default parameters. The valid reads were used to anchor super-scaffolds with Juicer (Durand et al., 2016) and 3d-dna pipeline (Dudchenko et al., 2017).