ncov
https://github.com/nextstrain/ncov
Python
Nextstrain build for novel coronavirus (nCoV)
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- Issues
- ENH: Add S1 mutations, reversion count and other branch colorings
- Allow a list of sequence exclusion files, instead of just one
- Delete pre-computed, downloaded input files on workflow completion on AWS Batch
- Fix annotate metadata with numeric strains
- Memory resource definitions
- Memory resource constraints are not passed to IQ-TREE (via `augur tree`)
- `annotate_metadata_with_index` raises `ValueError` when dtypes don't match
- Remove whitespace indents from large Auspice JSONs
- Fill in more lat/long data from the OpenStreetMap name-to-location API
- Visualise omicron recombinants
- Docs
- Python not yet supported