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Juicer is a tool that uses Hi-C sequencing reads as input and create normalized contact maps for visualization. The program has been used to visualize how assembly scaffolds should be reorganized following scaffolding with Hi-C data, which typically may still contain scaffolding errors. Besides being used as a tool for correcting scaffolding by Hi-C, the program is also used to detect 3D structure of the genome.




  • Operation: Scaffolding
  • Input: FASTQ
  • Output: -
  • Software interface: Command-line user interface
  • Language: Java, shell, AWK
  • Operating system: Linux, Mac OS X
  • License: Not stated
  • Cost: Free
  • Version name: 1.22.01
  • Credit: NIH New Innovator Award, NIH 4D Nucleome grant
  • Contact: erez _at_
  • Collection: -


Durand NC, Shamim MS, Machol I, Rao SS, Huntley MH, Lander ES, Aiden EL "Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments." Cell Syst, 2016
PMID: 27467249
PMCID: PMC5846465

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