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).