augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Replace custom deepdiff wrapper scripts with deepdiff CLI
- Report actual missing filename for index paths
- Refine scope of Augur's Python Development API
- Don't allow conflicting values when parsing metadata
- Ideas for improving how data flows through augur export v2
- Discussion: Should `augur mask` error if not a single change is made (no-op)?
- Internal representation of data
- Validate annotations produced from ancestral + translate
- BUG: Mask should not fail if no sites are to be masked
- dates: Consolidate date parsing logic
- Docs
- Python not yet supported