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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.




  • Operation: Scaffolding
  • Software interface: Command-line user interface
  • Language: awk, shell
  • Operating system: Linux, Mac OS X
  • License: The MIT licence
  • Cost: Free
  • Version name: -
  • Credit: Center for Theoretical Biological Physics, NIH New Innovator Award, NSF Physics Frontier Center Award, National Human Genome Research Institute (NHGRI) Center for Excellence for Genomic Sciences
  • Contact: erez _at_
  • Collection: -


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
PMID: 28336562
PMCID: PMC5635820

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