Comments (2)
For reference strains separating out DENV1-DENV4 (KM204119, KM204118, KU050695, and KR011349)) based on the following publication:
Añez, G., Heisey, D.A., Volkova, E. and Rios, M., 2016. Complete genome sequences of dengue virus type 1 to 4 strains used for the development of CBER/FDA RNA reference reagents and WHO international standard candidates for nucleic acid testing. Genome announcements, 4(1), pp.10-1128.
from dengue.
Documenting plan of work in the issue instead of scattered across PRs:
- Create a PR to prepare phylogenic workflow to be compatible with the nextclade workflow
- augur translate rooting to be compatible with nextstrain/nextclade#1455
- add a configurable
includes.txt
to force-include key strains (e.g. vaccine-related, lineage-defining)
- Rebase existing Nextclade dataset workflow PR
-
move shared resources into a dedicated "shared" directory b.c. 10 trees :lolcry:-> havenextclade workflow
link toconfig
andbin
dir inphylogenetic
since most should be the same. - Ask for expertise contributions from Nextclade Subject-Matter-Experts (SME)
-
- Use Sidney's strain_genotypes.tsv as the source of truth for Nextclade datasets in a separate PR
- Copy to config folder
- Map to Genbank accession to populate the
includes.txt
for the Nextclade workflow
from dengue.
Related Issues (17)
- Add E gene builds HOT 5
- Split by dengue serotype (denv1-denv4) HOT 1
- Harmonize with pathogen repo guide HOT 1
- 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 2
- 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
- Set root reference in phylogenetic builds
- ENH: nextclade extensions to display multiple nomenclatures
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from dengue.