Pangenome Browser
Project Website: GraphGenome.org
Before this Hackathon, the Graph Genome Browser Consortium was already working on implementing Pangenome Schematics: the first design capable of scaling to thousands of individuals in a single variation graph (a.k.a. Graph Genome). This hackathon will take the browser out of alpha stage and make it into a service useful for COVID-19 researchers.
Vision: Our goal is to provide a public server hosting Schematize browser loaded with an up to date COVID-19 pangenome with annotations on all our knowledge of variants and their effects aggregated across the globe. This global view of our current knowledge of the COVID-19 pangenome will be help enable faster access to data shared around the world. Virus sequence variation is relevant to vaccine targeting, virus tests, and triage.
- Josiah Seaman (coordinator)
- Simon Heumos (coordinator)
- Joerg Hagmann
- Ben Busby
- Pierre Marijon
- Toshiyuki Yokoyama
- 26+ participants
Join our Slack Channel: #pangenome_browser standard or from any Workspace
Extensive Documentation is available through graphgenome.org and on GitHub. A good place to start is introducing yourself and skills on slack and asking to be assigned an issue. There is also a technical paper with results in progress, but I need to get permission from all the other authors before sharing it.
- Issues can be found on our GitHub repositories which has Projects for tracking cross-repo features.
- Most issues are on the Schematize browser
- Deploy and local installation: Toshiyuki has created a pipeline which checkout the latest versions of our repo. This is the best option to start with. User-friendly installation is one of our development goals.
If you want to add comments please go to PangenomeBrowserOverview which is more interactive, too.
Sven Nahnsen and Simon Heumos from the Quantitative Biology Center were able to acquire deNBI Cloud resources for our project and hackathon.
The deNBI Cloud currently provides one VM of 28 cores, 64GB RAM and 1TB storage for our COVID19 Pangenome Visualization. The deNBI cloud covid-19-resources lists us as one of the available resources to fight COVID19.
This small VM will help us to create pangenome graphs and test our software. It is not meant for permanent data storage or permanent server hosting.
Simon Heumos will act as an admin for the cloud instance. Please see deNBI Usage Rules CovidViz for access instructions. Read the document carefully!