augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Improve Augur error handling
- augur subsample command
- Add warning to docs fetched by docs.nextstrain.org
- Format metadata in a tagged data format (e.g., JSON-LD)
- RFC: separating CLI and library code
- Add support for one or more sequence files as input to subcommands
- Allow users to override default columns names in metadata instead of using hardcoded column names
- Accept metadata in Microreact format
- Allow multiple metadata files as input to `--metadata`
- Refactor JSON Schema validation into new classes
- Docs
- Python not yet supported