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nextstrain
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seasonal-flu
Scripts. config, and snakefiles for seasonal-flu nextstrain builds
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Exclude sequences with unusual collection dates
#175
joverlee521
opened
2 weeks ago
2
Run pathogen-embed on HA/NA alignments to flag putative reassortant clades
#174
huddlej
opened
1 month ago
0
Summarize haplotype coverage by titer references using frequencies per haplotype from all available data
#173
huddlej
closed
4 weeks ago
0
Add representative samples from early clades to "broad" H1N1pdm HA Nextclade dataset
#172
huddlej
closed
1 month ago
0
Nextclade dataset for "broad" H1N1pdm HA misassigns early clade labels
#171
huddlej
closed
1 month ago
0
ci.yaml: Pin `pathogen-repo-ci`
#170
joverlee521
closed
2 months ago
0
Rename `master` to `main`
#169
genehack
opened
2 months ago
0
deploy-private-nextflu: Assume AWS role for short-lived credentials
#168
joverlee521
closed
2 months ago
0
Switch AWS credentials from a long-lived IAM user to short-lived role sessions
#167
tsibley
closed
2 months ago
0
inline root sequence
#166
rneher
closed
2 months ago
0
Upload trigger matrix
#165
joverlee521
closed
3 months ago
1
Use existing public 2y builds as “representative” trees in our reports
#164
huddlej
opened
3 months ago
0
Use a narrative template file to stub out a date-specific narrative for a given set of dated builds
#163
huddlej
opened
3 months ago
0
Plot counts per lineage by region with matplotlib instead of altair
#162
huddlej
closed
3 months ago
0
Use metadata from NA segment in joined metadata when HA segment isn't available
#161
huddlej
opened
4 months ago
0
Add isolate_id field to metadata
#160
huddlej
closed
4 months ago
0
Automate deployment of private nextflu.org site
#159
joverlee521
opened
4 months ago
0
Add GitHub Action for Nextclade annotations
#158
huddlej
closed
4 months ago
3
Trigger nextflu-private builds from upload action
#157
huddlej
closed
5 months ago
1
Update Suffolk lat/longs
#156
joverlee521
opened
5 months ago
0
"Suffolk" in `lat_longs.tsv` points to somewhere unexpected
#155
fanninpm
opened
5 months ago
1
Download clade definitions from GitHub
#154
huddlej
closed
6 months ago
0
profiles/nextstrain-public: Update build/auspice names
#153
joverlee521
closed
4 months ago
5
Rename public nextstrain builds to `seasonal-flu`
#152
joverlee521
closed
4 months ago
0
GISAID Quickstart: remove Conda runtime specific command
#151
joverlee521
closed
6 months ago
0
Add measurements panel for Welsh et al. escape scores
#150
huddlej
opened
6 months ago
0
Running issue nextstrain pipeline
#149
sekhwal
opened
6 months ago
18
Create PA-h3n2
#148
sekhwal
closed
6 months ago
1
Integrating FASTA Sequence into Influenza A/H3N2 Evolution Analysis and Visualizing in Nextclade
#147
sekhwal
closed
6 months ago
6
nextstrain.yaml: Update to Nextclade v3
#146
joverlee521
closed
6 months ago
0
Nextclade3 update
#145
rneher
closed
6 months ago
0
Filter low-quality sequences by Nextclade QC status
#144
huddlej
opened
6 months ago
0
Bump actions/setup-node from 3 to 4
#143
dependabot[bot]
closed
6 months ago
0
Bump actions/checkout from 3 to 4
#142
dependabot[bot]
closed
6 months ago
0
Version nextalign binary for transition
#141
victorlin
closed
7 months ago
1
Automatically deploy dated builds to nextflu-private group
#140
huddlej
closed
7 months ago
0
Add rules to the nextflu-private workflow to rename Auspice JSONs based on the build date and deploy the JSONs to the Nextstrain group
#139
huddlej
closed
7 months ago
0
Add Auspice JSON colorings for HA/NA accessions
#138
huddlej
closed
7 months ago
2
Export GISAID accessions from metadata into Auspice JSONs
#137
huddlej
closed
7 months ago
0
Update subclades
#136
rneher
closed
8 months ago
0
Add Welsh et al. epitope sites and escape scores
#135
huddlej
closed
6 months ago
0
Version nextclade binary for transition, i.e. nextclade -> nextclade2
#134
corneliusroemer
closed
7 months ago
0
Dmsa phenotype
#133
jgallowa07
closed
8 months ago
1
Add h3n2/na segment length to GFF
#132
jameshadfield
closed
8 months ago
0
Use Nextclade to assign clade labels in main phylogenetic workflow
#131
huddlej
opened
8 months ago
0
Automate monthly reports
#130
huddlej
opened
8 months ago
0
Make Markdown output for reports
#129
huddlej
closed
8 months ago
1
Update clades
#128
huddlej
closed
9 months ago
0
Revisit deploy-private-nextflu Netlify CLI version pin
#127
joverlee521
opened
9 months ago
0
Fix deploy private
#126
joverlee521
closed
9 months ago
1
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