This is the documentation page for GenomeView.
GenomeView is a stand-alone genome browser and editor initiated in the BEG group at VIB, then further developed at Broad Institute and currently maintained at TU Delft. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard file formats are supported.
GernomeView offers
- Genome browser
- Short read alignment visualization
- Multiple alignment viewer
- Comparative genomics
- NGS (Next Generation Sequencing) viewer
- Annotation editor
- Easy integration with existing websites and data platforms
- Authentication and encryption
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Recommended system specs:
- 2 Gb of memory, minimum is 1 Gb
- dual-core or better processor, but GenomeView will work with less.
- To browse online data, it's recommended to have a high-speed, low-latency connection
- Recent version of Windows, *nix or Mac OS
- Recent version of Java 17+.
- Install java 18 or higher if it's not yet installed.
- You can check by running 'java -version' in the commandline.
- You can get an installer from http://www.java.com or https://openjdk.org/.
- On linux you can
sudo apt install openjdk-17 - If you only want to run java you can install the
JRE, for compilation you should install theJDK.
- Go to https://artifactory.ewi.tudelft.nl/ui/native/libs-release/net/sf/genomeview
- Click the version you need, probably the highest version number available.
- download the jar-with-dependencies.jar file and store it at a convenient place on your computer.
- Start the app, using one of the following
- double click on the jar file to start the app. This will run with the default memory.
- on the commandline with
java -Xmx4g -jar genomeview.jar. You can change the '4g' into a bigger number if you need more memory in GenomeView.
Tip
'double click to start' may require you to set the jar file to 'executable' and/or
setting the default application for 'jar' files.
On Linux for example, right click on the jar, "Open with other Application",
select "use a custom command" and enter java -jar in the text box. Then click open.
GenomeView log files are in the folder .genomeview (dot genomeview) in your home folder of your local computer.
- On MS Windows versions this is
C:/Users/[username]/.genomeview - On Mac and Linux this is
~/.genomeview
If you can still start GenomeView, you can find the exact location under the 'Help menu' > 'About'
We have several manuals for you
The source code is available on http://github.com/genomeview/genomeview. .