GenomeFlow : A Graphical Tool for Modeling and Analyzing 3D Genome Structure

A comprehensive graphical tool to facilitate the entire process of 3D genome organization, modeling and analysis of Hi-C data.

GenomeFlow is capable of creating index for reference genome, generating maps from raw fastq data files, and reconstructing two-dimensional (2D) and three-Dimensional (3D) chromosome and genome models with a graphical user interface.

If you have further difficulties using GenomeFlow, please do not hesitate to contact us (chengji@missouri.edu)

Documentation

Please see the wiki for an extensive documentation, or download the user guide

Distribution

In this repository, we include the folowing:

• executable: contains sample datasets. Download latest version of the GenomeFlow executable from here
• src: contains the GenomeFlow source codes
• user_guide: contains user guide
• lib: contains the external libraries used in source code

Hardware and Software Requirements

GenomeFlow consists of three parts: the pipeline that takes raw fastq files to create a formatted text files called the 1D-Functions, the analysis of binned Hi-C file called 2D-Functions, and three-dimensional (3D) models analysis called 3D-Functions tools.

Requirements

GenomeFlow requires the use of a computer, with ideally >= 4 cores (min 1 core) and >= 4 GB RAM (min 2 GB RAM)

GenomeFlow tools requirements

The minimum software requirement to run GenomeFlow is a working Java installation (version >= 1.7) 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

Burrows-Wheeler Aligner (BWA) for 1D-Function

The latest version of BWA should be installed from http://bio-bwa.sourceforge.net/.

Bowtie2 for 1D-Function

The latest version of Bowtie2 should be installed from http://bowtie-bio.sourceforge.net/index.shtml

Samtools for 1D-Function

The latest version of Bowtie2 should be installed Samtools (http://samtools.sourceforge.net/)

Installation Instructions for BWA, Bowtie2, and Samtools can be found here

Building from source code

The project uses JUnit for testing and Maven to manage dependencies and builds. It can be imported into Eclipse as a Maven project.

Requirements

• Maven: manage builds and dependencies.
  If using Eclipse, there is no need to install Maven. Otherwise, Maven needs to be installed to compile the code.

• Example commands
  mvn compile: to compile
  mvn test: to run test
  mvn package: to compile, test and package
  

Compiling source code

Requires Java JDK 1.8 (not JRE but JDK, set JAVA_HOME to JDK folder)