augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
Triage Issues!
When you volunteer to triage issues, you'll receive an email each day with a link to an open issue that needs help in this project. You'll also receive instructions on how to triage issues.
Triage Docs!
Receive a documented method or class from your favorite GitHub repos in your inbox every day. If you're really pro, receive undocumented methods or classes and supercharge your commit history.
Python not yet supported38 Subscribers
Add a CodeTriage badge to augur
Help out
- Issues
- augur clade only partially assigns clade information
- ENH(clades): Validate `clades.tsv`, bad file currently throws uncaught error
- ENH(tree): See whether we can add Usher and/or Maple as experimental tree builders for augur tree
- DOC(filter): Surface excellent function level documentation`--exclude-where` for cli help
- filter: Improperly handled `ValueError: not enough values to unpack (expected 2, got 1)` in ` _parse_filter_query`
- Report helpful error if filter query string malformed
- DOC(curate): Improve explanation of what `--seq-field` does
- BUG: Passing unrecognized argument shows general augur not subcommand usage string
- DOC(parse): Not clear from docs how `--prettify-fields` works
- ENH(curate): Support zstd compressed fasta, metadata and/or ndjson
- Docs
- Python not yet supported