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.
Detailed documentation on building, installation, usage is available at
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
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 <YOUR_NGS_DATA_FOLDER> 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
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
developbranch - each commit): Development versions
- 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
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
# Build NGB as a standalone JAR file with Command Line Interface tools
$ ./gradlew buildJar buildCli
# Build docker with documentation
$ ./gradlew buildDocker buildDoc