augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- How to have more control over the contents of the maintainers section?
- [BUG] augur mask only supports VCFs with a single "chromosome" entry
- Developer Documentation for Functions Generating 'Auto-Colorbys'
- Define concept of strain, date etc in docs
- Document file formats
- Start and end date of augur build intervals are not stored in auspice JSONs
- Make Sequence Traits work with Fasta Input
- Store titer records in TiterRecord class and export in structured JSON format
- Representation of uncertainty in JSONs
- augur export prefers num_date over numdate exported by augur refine
- Docs
- Python not yet supported