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.
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 https://doi.org/10.1016/j.cels.2016.07.002
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