augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Add sqlite3 cli to augur's bioconda recipe once augur merge PR is merged
- Pick a meaning of TSV and use it consistently
- No standard test environment
- [traits] cmd should warn when metadata is completely missing for a given node
- augur curate: improve metadata header parsing
- chore(deps): allow numpy v2
- Update pinned dependencies
- chore(deps): configure dependabot for pip deps
- augur curate rename: Add option to drop fields/columns
- Improve help output for augur curate subcommands
- Docs
- Python not yet supported