nextstrain/seasonal-flu

Issues

• Automate monthly reports

  #130 opened 8 months ago by huddlej
  0

• Use existing public 2y builds as “representative” trees in our reports

  #164 opened 2 months ago by huddlej
  0

• Use a narrative template file to stub out a date-specific narrative for a given set of dated builds

  #163 opened 2 months ago by huddlej
  0

• Plot counts per lineage by region with matplotlib instead of altair

  #162 opened 2 months ago by huddlej
  0

• Rename public nextstrain builds to `seasonal-flu`

  #152 opened 3 months ago by joverlee521
  0

• Use metadata from NA segment in joined metadata when HA segment isn't available

  #161 opened 3 months ago by huddlej
  0

• Automate deployment of private nextflu.org site

  #159 opened 4 months ago by joverlee521
  0

• Running issue nextstrain pipeline

  #149 opened 5 months ago by sekhwal
  18

• "Suffolk" in `lat_longs.tsv` points to somewhere unexpected

  #155 opened 5 months ago by fanninpm
  1

• Integrating FASTA Sequence into Influenza A/H3N2 Evolution Analysis and Visualizing in Nextclade

  #147 opened 5 months ago by sekhwal
  6

• CDS coordinates are incorrect for Vic and Yam hemagglutinin

  #57 opened 5 months ago by huddlej
  1

• Filter low-quality sequences by Nextclade QC status

  #144 opened 6 months ago by huddlej
  0

• Unable to run nextstrain command under 'Quickstart with GISAID data'

  #125 opened 6 months ago by swantan
  3

• Annotate Nextstrain clade names by default with official full clade names as alternate annotation

  #74 opened 6 months ago by huddlej
  2

• Use nextalign instead of custom Python codon alignment script

  #64 opened 6 months ago by huddlej
  3

• 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 opened 6 months ago by huddlej
  0

• Export GISAID accessions from metadata into Auspice JSONs

  #137 opened 7 months ago by huddlej
  0

• Use Nextclade to assign clade labels in main phylogenetic workflow

  #131 opened 8 months ago by huddlej
  0

• select_strains.py fails if metadata age column has missing values

  #72 opened 8 months ago by philipshirk
  1

• Annotate titers per node

  #90 opened 8 months ago by huddlej
  1

• Use augur filter --min/max-date

  #83 opened 8 months ago by joverlee521
  1

• Revisit deploy-private-nextflu Netlify CLI version pin

  #127 opened 8 months ago by joverlee521
  0

• Example build not working. MissingRuleException

  #112 opened a year ago by limh25
  6

• Upload metadata.tsv for downstream use

  #107 opened a year ago by corneliusroemer
  1

• H3N2 NA aa length is wrong

  #98 opened a year ago by ammaraziz
  6

• Assign clades to nodes via tabular metadata

  #91 opened 2 years ago by uee9
  0

• Instructions for custom flu dataset

  #88 opened 2 years ago by limh25
  1

• Explore use of IQ-TREE's constraint tree option

  #79 opened 2 years ago by joverlee521
  1

• Minor typo in README: "depending on the assay that passage history of the antigens"?

  #77 opened 3 years ago by corneliusroemer
  0

• Add "division"-level geographic resolution to Auspice JSONs

  #70 opened 3 years ago by huddlej
  1

• Refactor workflows to follow Nextstrain standards from ncov workflow

  #58 opened 4 years ago by huddlej
  2

• Identify "prototype virus" for each putative clade

  #66 opened 3 years ago by huddlej
  0

• Annotate more granular clades on nextflu site

  #65 opened 3 years ago by huddlej
  0

• Use FRA data instead of HI data for live H3N2 builds

  #62 opened 3 years ago by huddlej
  1

• Divergence tree does not display properly on the x-axis for nextflu site

  #61 opened 3 years ago by huddlej
  4

• Create dated copies of 2y builds

  #63 opened 3 years ago by huddlej
  0

• Some strain names in titer records are misspelled

  #60 opened 3 years ago by huddlej
  0

• Color strains by database submission date

  #55 opened 3 years ago by huddlej
  1

• Strains with ambiguous dates are assigned two different dates in auspice output

  #48 opened 5 years ago by huddlej
  0

• Estimate tip frequencies up to the month of latest available strains

  #54 opened 4 years ago by huddlej
  0

• Annotate new clades for H3N2 and H1N1pdm

  #52 opened 4 years ago by huddlej
  3

• [Feature request] Add most recent Northern Hemisphere vaccine strains to builds

  #49 opened 4 years ago by huddlej
  1

• The json files exported by augur can not be visualized by the auspice

  #51 opened 4 years ago by sunshine1126
  3

• subsampling in flu

  #38 opened 5 years ago by rneher
  0

• Epitope and non-epitope coloring for H1N1pdm NA broken

  #33 opened 5 years ago by trvrb
  1

• Prioritize rather than filter to "complete" genomes

  #24 opened 5 years ago by trvrb
  1

• Batched WHO jobs exceed disk limit of AWS instances

  #28 opened 5 years ago by barneypotter24
  3

• how to plot the following figure?

  #27 opened 5 years ago
  2

• Enable preferred sampling of specific regions during strain selection

  #20 opened 5 years ago by huddlej
  0

• Substitution model not loading on nextflu/auspice

  #22 opened 5 years ago by trvrb
  5