augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- [curate apply-geolocation-rules] treat '?' values akin to empty values
- refine: warn if doing timetree and there's apparent mismatch between metadata and sequence ids
- New command: `augur curate apply-date-bounds`
- chore: Some typing-related improvements
- Aligner extra args
- Simplify configuration of `accession` as metadata id column
- Weighted sampling stdout/err is very verbose: multiple screens of warnings
- 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
- Docs
- Python not yet supported