NGB

New Genome Browser (NGB) is a Web client-server tool that has been developed with the several key distinctive features in mind:

• Visualization of Structural Variations (SVs) and their supporting reads
• Performance and scalability while working with big/cloud genome data
• CRAM format support
• Integration with various data sources, including ENSEMBL, UniPROT and other internal/external databases
• User experience that is based on a set of useful features like hotkeys, variation tables, docking widgets, etc.
• Web 3D molecular viewer integrated

We have done our best to make those features at the highest possible level and thus make NGB one the best web-based genome browser. The community lead by EPAM intends to develop NGB extending it functionality and improving user experience. Your suggestions and comments are welcome.

We believe that NGB (being a namesake of a Neuroglobin (NGB) gene, coding a protein that is involved in oxygen transport in the brain) will help researchers and clinicians to discover the valuable insights in the huge volumes of genomic data.

Documentation

Detailed documentation on building, installation, usage is available at

• Markdown sources
• Latest HTML documentation

Publications

Links to publications that contain NGB references

• Prioritisation of structural variant calls in cancer genomes
• Dataset visualization for article Prioritisation of Structural Variant Calls in Cancer Genomes

Quickstart

Docker image is used to build and run NGB for a quickstart. Other build and run options are described at installation section of NGB documentation

Make sure docker is installed

$ docker --version
Docker version 1.12.5

If docker is not installed, please follow docker engine installation guide for your operating system

Get NGB sources

$ git clone https://github.com/epam/NGB.git
$ cd NGB

Build sources and package binaries into docker container

$ ./gradlew buildDocker

Image with name ngb:latest will be created. Verify that it was created correctly

$ docker images
REPOSITORY      TAG     IMAGE ID        CREATED         SIZE
ngb             latest  356774a063ad    2 minutes ago    564.4 MB

Run NGB from a created image

Replace placeholder with a real path to a folder with NGS data

$ docker run -p 8080:8080 -d --name ngbcore -v <YOUR_NGS_DATA_FOLDER>:/ngs ngb:latest

Verify that NGB is up and running: navigate with your web-browser to http://localhost:8080/catgenome

Please note that the following web-browsers are supported at the moment

• Chrome (>= 56)
• Firefox (>= 51)
• Safari (>= 9)
• EDGE (>= 25)

Default NGB page should be shown

That's it. Now NGS files could be added and viewed. Please refer to NGB Command Line Interface - Typical tasks to register genome and NGS files

Prebuilt binaries

NGB binaries can be retrieved from the following locations:

• Releases:
  • GitHub Releases: https://github.com/epam/NGB/releases
  • Direct HTTP links: Release versions
• Development builds (created from develop branch - each commit): Development versions

How to build NGB

Requirements

• Oracle JDK 8 or Open JDK 8
• Node.js = 6.9.5
• Docker engine used to build docker images, if it is not a case - then could not be installed
• MkDocs >= 0.16.0 and mkdocs-material used to build documentation, if it is not a case - then could not be installed

General build process

Gradle build script is provided for building NGB components

$ ./gradlew [tasks]

Available tasks:
buildWar        builds java web application archive, containing client and server binaries
buildCli        builds ngb command line interface, used to manipulate data within ngb
buildDocker     builds jar-file and packages it into a docker image, using docker/core/Dockerfile
buildDockerDemo builds "core" docker image and initilizes it with demo data, using docker/demo/Dockerfile
buildDoc        builds markdown documents into html web-site
buildJar        builds standalone jar-file with embedded Tomcat
buildDesktop    builds standalone desktop NGB application
buildAll        builds all components, listed above

All tasks could be combined.

Build artifacts are placed into dist/ folder in a root level of a cloned repository

If this script does not fit - each component could be built on it's own. Build process for each component is described in a appropriate README file, located in the component's folder

Examples for typical tasks

# Build NGB as a standalone JAR file with Command Line Interface tools
$ ./gradlew buildJar buildCli

# Build docker with documentation
$ ./gradlew buildDocker buildDoc