Related Issues (20)
- Modernize `ncbi-field-map` in config
- Bug: Update dropped strains file to list accession instead of strain HOT 5
- ENH: Generalize taxon id to serotype map definitions to a configuration file
- Removal of genome containing plasmid sequence HOT 16
- Establish some deduplication guidelines within the phylogenetic workflow HOT 1
- Switch DENV2 genotypes to numeric to be consistent with DENV1, 3, and 4 HOT 3
- Add manual serotype annotations along with justifications to "annotations.tsv" HOT 1
- Rename "subtype" to "genotype" HOT 5
- The `phylogenetic` github action cannot build from staged `ingest` data during dev-branch testing
- Update the links of FASTA and metadata in the README HOT 1
- Word of caution for genome MT597439 HOT 5
- ENH: nextclade extensions to display multiple nomenclatures
- Fine tune the "Dengue virus DENVx genotypes" dataset HOT 1
- Improve serotype assignment in Dengue virus DENVx genotypes datasets
- Restructure S3 URLs
- ingest: use new augur curate commands
- Use a "scripts" directory instead of a "bin" directory
- Rename `config` to `defaults`
- phylogenetic: Stochastic augur refine error
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