augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Allow user to exclude specific strains from refine's clock filter
- Revisit CI check-docs + `/devel/generate-developer-api-docs`
- curate rename: does not work if some fields do not exist
- curate apply-geolocation-rules: Fails when fields contain `null` values
- Composable auspice config
- Remove export v1
- align: trim down print statements for insertions
- tree: automatically remove intermediate files with option to disable clean up
- Help text indentation renders differently in rendered docs vs. `--help` output
- Standardize error handling and console output functions
- Docs
- Python not yet supported