2.4 Hi-C library construction and chromosome assembly
The raw reads produced by the illumina High-throughput sequencing
platform based on the technology of sequencing by synthesis were
filtered by SOAPnuke software (Chen et al., 2018). Juicer was employed
to compare the obtained clean reads to genome draft (Durand et al.,
2016). After filtering the results and removing the misaligned reads,
3d-DNA software was applied to preliminarily cluster, order, and orient
the unique, valid interaction pairs onto the pseudochromosomes
(Dudchenko et al., 2017). Juicer-box was used to correct
pseudochromosomes to improve chromosome assembly level. For the
evaluation of the Hi-C assembly results, the final pseudochromosome
assemblies were divided into 100 kb bins of equal lengths and a heat map
was obtained to visualize the interaction signals generated by the valid
mapped read pairs between each bin.