augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Missing escape of square brackets causes diff_jsons.py in some cram tests to be false negative
- fix(tests): Fix false negative cram tests
- tests: add cram wrapper parallel_cram.sh that runs cram tests in parallel
- feat(ancestral): make --genes optional when reconstructing translations, if omitted, translate all genes in annotation
- feat(ancestral): Add optional Nextclade GFF3 compatibility mode
- Layering Auspice config files
- Validation regex pattern for `branch_label` display default values in Auspice config JSON is too strict
- CLI help text can't contain rST section headings
- Gff3 file: differences between nextclade datasets and augur ancestral
- Improve help text of CLI options that use `extend` and `ExtendOverwriteDefault` actions
- Docs
- Python not yet supported