De novo genome assembly and Hi-C scaffolding
All of the filtered Nanopore reads were used for the draft genome
assembly in Nextdenovo software (v2.3.1;
https://github.com/Nextomics/NextDenovo) with default parameters. The
assembled genome was corrected using the filtered Illumina genome reads.
BWA software (BWA-MEM module) (Li &
Durbin 2009) was used to map short reads to the genome, and Pilon
software (Walker et al. 2014) was
used for error correction of the sequenced bases. To obtain the
chromosome-level genome, the Hi-C reads were aligned to the assembled
genome using Juicer software. The software 3D-DNA
(Dudchenko et al. 2017) was used
to cluster scaffolds into different clusters; in each group, the order
of scaffolds was determined by the strength of interactions. Finally,
all the possibilities of scaffold orientation and generated finely
orientated scaffolds using a weighted directed acyclic graph.