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
- DOC(curate): Not obvious at first glance that ndjson is default in/output format
- ENH(parse): Support gz/xz/zstd compressed sequences/metadata for IO and/or output to stdout (to allow compression in pipe)
- DOC(passthru normalize-strings): Unclear from docs how the command works
- 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
- Docs
- Python not yet supported