Germany
April 1, 2020
Towards browsing the global genetic variation of SARS-CoV-2
Computomics, together with project partners at QBiC and academic collaborators around the globe will actively help overcome the Corona crisis by elucidating and making publicly available the global genomics of SARS-CoV-2.
Within the scope of a Covid-19 virtual biohackathon, officially starting next week from April 5-11, we will help advance the PantoGraph pangenome viewer, which has already being developed by an international team of fantastic researchers around the globe and us.
The overarching goal of the biohackathon is to build a publicly available resource containing all genomic variation of the virus found in Covid-19 patients around the world and visualizing them using the novel PantoGraph concept. The participants will be working towards building a pipeline where raw (short) reads of new virus sequences can be uploaded and aligned against a genome graph, containing all the already sequenced strains, to visually compare them against the global pangenome of SARS-CoV-2. Further efforts will include metadata integration like disease symptoms, severeness, or geographic origin to compare virus subpopulations and potentially link genetic variants to certain symptoms.
This on-the-fly analysis and comprehensive representation of the global SARS-CoV-2 genetics will be unique and will help identify cases where the PCR test or a future vaccine might not target mutated viruses anymore. The latest study on SARS-CoV-2 genetic variation already found structural rearrangements happening in two cases in China. These altered sequences are not present in the single reference strain, and so aligning to a graph structure is utterly important to fully capture the virus’ variability.
The hackathon is open for everyone. If you like to contribute to this software project, please feel free to join us fight Covid-19: register for the biohackathon and/or join our Pangenome Visualization group: graphgenome.org, the group is already actively coding. Most beneficial skills for PantoGraph include JavaScript experience.
We want to give a big thanks to our supporter - the deNBI Cloud - who are providing a VM of 28 cores, 64GB RAM and 1TB storage for our COVID19 Pangenome Visualization.
Donations for infrastructure are welcome as well.
For more information please contact us.
Be well!
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