About
The JBrowse 2 genome hubs were created by bulk importing UCSC data to create annotation-rich JBrowse data resources. We created scripts for parsing UCSC MySQL database dumps for the main UCSC genome browser sets, and for converting hub.txt files to JBrowse config.json files for the GenArk configs
Citing resources
If you use these resources in your publication, please consider citing:
- JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biology (2023). https://doi.org/10.1186/s13059-023-02914-z
- GenArk: towards a million UCSC genome browsers. Genome Biology (2023). https://doi.org/10.1186/s13059-023-03057-x
Further resources
- Further citations for UCSC resources: https://genome.ucsc.edu/cite.html
- Credits for individual UCSC species: https://genome.ucsc.edu/goldenpath/credits.html
- License of UCSC data and resources: https://genome.ucsc.edu/license/
FAQ
- Why not use the UCSC REST API?
- Using bulk import gives us more control and allows us to create a native JBrowse 2 experience instead of designing an extensive compatibility layer. The UCSC REST API is rate limited and also not comprehensive for all the types of data we want to access
- Why not parse the track hub (hub.txt) files directly?
- UCSC does not have hub.txt files for their main browsers, like hg19 and hg38, so adding a bulk import process was the easiest way to make browsers with access to their datasets
- Are there any restrictions for using this database?
- All data is freely available for commercial and non-commercial use, except for liftOver files, which have a non-commericial use restriction, following the note placed here https://genome.ucsc.edu/license/
Thanks!
We want to sincerely thank the UCSC Genome Browser team for their great work and open licensing of data resources
Contact
Feel free to contact or report issues, the main github repo for this project is here https://github.com/cmdcolin/jb2hubs/
More contact info here https://jbrowse.org/jb2/contact/