augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- ENH(parse): Allow specification of which field to retain as sequence id, e.g. accession instead of strain name
- `augur translate` produces genome annotations that fail validation in `augur export`
- Add reference docs for `lbi` and `titers`
- read_metadata: Inconsistent behavior with missing and extra metadata columns
- ENH: Add `augur colors` subcommand based on `assign-colors.py` scripts
- Consolidate CI and Release jobs
- Fix order of exported colorings from augur export v2 when color by metadata is used
- Update existing cram tests with new practices
- Import: Proposed config template is outdated, uses deprecated names
- measurements collection configuration JSON cannot specify "fields" that reference columns used for `--key` or `--value`
- Docs
- Python not yet supported