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nextstrain
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dengue
Nextstrain build for dengue virus
https://nextstrain.org/dengue
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Use scripts
#76
j23414
closed
9 hours ago
0
Use a "scripts" directory instead of a "bin" directory
#75
j23414
closed
9 hours ago
0
ingest: use new augur curate commands
#74
joverlee521
opened
5 days ago
0
Restructure s3 urls
#73
j23414
opened
6 days ago
0
Restructure S3 URLs
#72
joverlee521
opened
1 week ago
0
Add description
#71
j23414
closed
1 week ago
0
Improve serotype assignment in Dengue virus DENVx genotypes datasets
#70
j23414
opened
2 weeks ago
0
Fine tune the "Dengue virus DENVx genotypes" dataset
#69
j23414
opened
3 weeks ago
1
Adds a reference to the GenBank data source
#68
j23414
closed
3 weeks ago
0
Setting an outgroup for the "Dengue virus DENVx genotypes" dataset
#67
j23414
closed
2 weeks ago
1
drop unalignable example sequences
#66
j23414
closed
2 weeks ago
1
fixup: Standardize nextclade dataset names
#65
j23414
closed
1 month ago
0
hot fix: fill in READMEs for the Nextclade dataset
#64
j23414
closed
1 month ago
1
feat: remove word "dataset" from Nextclade dataset names
#63
ivan-aksamentov
closed
1 month ago
1
Manually fix serotype mis-annotations
#62
j23414
closed
1 month ago
0
Hotfix: Infer ancestral root in the phylogenetic workflow
#61
j23414
closed
1 month ago
0
Switch AWS credentials from a long-lived IAM user to short-lived role sessions
#60
tsibley
closed
1 month ago
0
ENH: nextclade extensions to display multiple nomenclatures
#59
j23414
opened
1 month ago
0
Fine tuning the Nextclade all dataset
#58
j23414
closed
1 month ago
3
Prepare phylogenetic workflow for Nextclade workflow
#57
j23414
closed
1 month ago
0
Set root reference in phylogenetic builds
#56
j23414
closed
1 month ago
0
Fix serotype annotation for MT597439
#55
j23414
closed
1 month ago
0
Word of caution for genome MT597439
#54
Rohit-Satyam
closed
1 month ago
5
Fixup: update the links of FASTA and metadata in the README
#53
j23414
closed
1 month ago
0
Update the links of FASTA and metadata in the README
#52
Rohit-Satyam
closed
1 month ago
1
Consistent serotype-genotype column names and auspice color titles
#51
j23414
closed
1 month ago
0
Add configurable staged input files for the `phylogenetic` github action
#50
j23414
closed
1 month ago
0
The `phylogenetic` github action cannot build from staged `ingest` data during dev-branch testing
#49
j23414
closed
1 month ago
0
Use gene reference files to generate E gene trees
#48
j23414
closed
1 month ago
0
Generate gene reference files
#47
j23414
closed
2 months ago
1
hotfix: display genbank accession link in node popup box
#46
j23414
closed
2 months ago
1
Dynamically generate the auspice config files
#45
j23414
closed
2 months ago
3
Instead of '?', set default gene_coverage to 0
#44
j23414
closed
2 months ago
1
Add independent ingest and phylogenetic GH Action workflows
#43
j23414
closed
2 months ago
1
phylogenetic: Use inline root sequence
#42
joverlee521
closed
2 months ago
3
Rename "subtype" to "genotype"
#41
j23414
closed
1 month ago
5
Fix phylo input
#40
joverlee521
closed
2 months ago
7
Update ncbi_serotype annotations for flagged records
#39
j23414
closed
3 months ago
0
Automate ingest and phylogenetic workflows
#38
j23414
closed
3 months ago
3
Add nextstrain-automation build-configs to phylogenetic worklfow
#37
j23414
closed
3 months ago
0
Add gene coverage columns during ingest workflow
#36
j23414
closed
2 months ago
1
Harmonize ingest with pathogen repo guide
#35
j23414
closed
3 months ago
0
Cleanout unused slack and trigger rebuild rules
#34
j23414
closed
3 months ago
0
Add manual serotype annotations along with justifications to "annotations.tsv"
#33
j23414
closed
2 months ago
1
Switch DENV2 genotypes to numeric to be consistent with DENV1, 3, and 4
#32
j23414
opened
3 months ago
3
Add a CHANGELOG
#31
j23414
closed
4 months ago
0
Establish some deduplication guidelines within the phylogenetic workflow
#30
j23414
opened
4 months ago
1
Exclude circular synthetic (or chimeric) sequences
#29
j23414
closed
4 months ago
1
Removal of genome containing plasmid sequence
#28
Rohit-Satyam
closed
2 months ago
16
ENH: Generalize taxon id to serotype map definitions to a configuration file
#27
j23414
opened
4 months ago
0
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