augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- [Feature request] GPU acceleration?
- [BUG] augur mask only supports VCFs with a single "chromosome" entry
- [BUG] AttributeError can be thrown by the run function in augur/traits.py
- WIP and RFC: Rewrite `filter.py` with several classes
- [WIP] Add tests for clades and add black code format
- Developer Documentation for Functions Generating 'Auto-Colorbys'
- Define concept of strain, date etc in docs
- Document file formats
- Start and end date of augur build intervals are not stored in auspice JSONs
- Update the conda channels list in environment.yml
- Docs
- Python not yet supported