3D-DNA is a tool to scaffolding contigs using Hi-C reads. It implements iterative scaffolding and mis-assembly detection as the core of the pipeline. It can also perform genome polishing and merging assembly to give chromosome-scale scaffolds.
Scaffolding
Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL "De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds." Science, 2017 https://doi.org/10.1126/science.aal3327
PMID: 28336562
PMCID: PMC5635820
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