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De novo genome scaffolding using Hi-C is the area I'm least familiar with. Hope others will comment. In a meantime, can recommend papers from Phase Genomics company, they specialize in genome scaffolding: https://phasegenomics.com/publications/#papers. They also have a software FAQ, https://phasegenomics.com/resources/#faq_software, and a documentation with recommendations on scaffolding, https://phasegenomics.github.io/
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More tools for de novo genome assembly from Hi-C reads: https://omictools.com/assembly-scaffolding-1-category
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