About Juicebox

Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is available on the wiki. Instructions below pertain primarily to usage of command line tools and the Juicebox jar files.

Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juicebox Assembly Tools Module website https://aidenlab.org/assembly for more details on how to use Juicebox for assembly.

Juicebox was created by Jim Robinson, Neva C. Durand, and Erez Lieberman Aiden. Past contributors include Ido Machol, Zulkifl Gire, Marie Hoeger, Fanny Huang, Nam Hee Kim, Vi Nguyen, Jay Ryu, Nathaniel T. Musial, and Ragib Mostofa.

Ongoing development work is carried out by Muhammad Saad Shamim, Neva C. Durand, and Olga Dudchenko.


For FAQs, or for asking new questions, please see our forum: aidenlab.org/forum.html.

IntelliJ Setup

Use IntelliJ IDEA (Community edition - free)

To set up in IDEA, have the Java SDK installed then you'll point to it (IntelliJ has lots of documentation on this sort of thing).

Hardware and Software Requirements

The minimum software requirement to run Juicebox is a working Java installation (version > 1.6) on Windows, Linux, and Mac OSX. We recommend using the latest Java version available, but please do not use the Java Beta Version. Minimum system requirements for running Java can be found at https://java.com/en/download/help/sysreq.xml. To download and install the latest Java Runtime Environment (JRE), please go to https://www.java.com/download.

We recommend having at least 2GB free RAM for the best user experience with Juicebox.

To launch the Juicebox application from command line, type java -Xms512m -Xmx2048m -jar Juicebox.jar

Note: the -Xms512m flag sets the minimum memory heap size at 512 megabytes, and the -Xmx2048m flag sets the maximum size at 2048 megabytes (2 gigabytes). These values may be adjusted as appropriate for your machine.


We have extensive documentation for how to use Juicebox at https://github.com/theaidenlab/juicebox/wiki including a video, a Quick Start Guide, and a detailed tutorial.

For using Juicebox to assemble genomes see https://www.aidenlab.org/assembly/.

Command Line Tools Usage

See the documentation at https://github.com/theaidenlab/juicer/wiki for information on how to use the Juicer tools.

Compiling Jars from Source Files

  1. You should have Java 1.8 JDK and Apache Ant installed on your system. See below for more information.
  2. Go to the folder containing the Juicebox source files and edit the juicebox.properties file with the proper Java JDK Address.
  3. Open the command line, navigate to the folder containing the build.xml file and type ant The process should take no more than a minute to build on most machines.
  4. The jars are written to the directory out/. You can change this by editing the build.xml file.

For Windows/Mac/Linux, the Java 1.8 JDK can be installed from here: https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html (Alternative) For Ubuntu/LinuxMint https://tecadmin.net/install-oracle-java-8-jdk-8-ubuntu-via-ppa/

Windows Installing Ant requires some minor changes to your system environment. Follow the instructions in this article: https://www.nczonline.net/blog/2012/04/12/how-to-install-apache-ant-on-windows/

Linux In the command prompt, type sudo apt-get install ant or sudo yum install ant depending on your package installer