augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Improve CLI help text
- `augur merge` is slow to read in metadata
- parse: Prefer `strain` over `name` as sequence ID field
- Set pipefail for cram tests
- filter: Deprecate `--output` and `-o`
- merge: Import metadata files concurrently?
- Release: changelog can be out-of-sync
- Align fractional sequences per group conversion methods
- Legacy editable installs are deprecated
- Revise docs for v25 features to add `versionadded` directives
- Docs
- Python not yet supported