Welcome to Juicer!

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments


End-to-End Pipeline

Juicer is our end-to-end automated pipeline for converting raw reads into Hi-C maps and loop calls - using only a single command! Check out the documentation here!


Command Line Tools

Use command line tools to analyze your own maps and export data! Check out the documentation and download the latest jar.

Cluster Support


Open Source

Juicer has been released Open Source under the MIT License! Fork us on Github!

Juicer is currently in its alpha release. Please contact us if you have questions, need help with the set up, or have bug reports. You can also report bugs via Github Issues.

Citing Juicer

If you use Juicer in your research, please cite:

Neva C. Durand*, Muhammad S. Shamim*, Ido Machol, Suhas S. P. Rao, Miriam H. Huntley, Eric S. Lander, and Erez Lieberman Aiden. "Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments." Cell Systems 3(1), 2016.

Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, Ido Machol, Arina D. Omer, Eric S. Lander, Erez Lieberman Aiden. "A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping." Cell 159, 2014.

* contributed equally