Issues

• Suggestion to designate SW.2.1 as major clade

  enhancement
  nextstrain/ncov#1222 · Filter by author xz-keg opened on Jul 30, 2026
  1

• Replace combine_metadata.py with augur merge

  breaking
  nextstrain/ncov#1196 · Filter by author victorlin opened on Jan 31, 2026
  1

• Ensure BA.3.2 shows up on all-time builds not just recent ones

  enhancement
  nextstrain/ncov#1191 · Filter by author corneliusroemer opened on Dec 8, 2025

• Properly handle CSV-like TSVs

  nextstrain/ncov#1165 · Filter by author joverlee521 opened on Dec 6, 2024

• Use weighted sampling

  enhancement
  nextstrain/ncov#1141 · Filter by author victorlin opened on Aug 14, 2024
  2

  

• Improve / standardize the way that we pass through default parameters and build-specific parameters

  enhancement
  nextstrain/ncov#1131 · Filter by author trvrb opened on Jul 26, 2024
  6

• Define workflow dependencies

  nextstrain/ncov#1118 · Filter by author victorlin opened on Jun 25, 2024

• Rename master to main

  enhancement
  nextstrain/ncov#1116 · Filter by author genehack opened on Jun 13, 2024

• Port CI to pathogen-repo-ci GH Action workflow

  enhancement
  nextstrain/ncov#1109 · Filter by author genehack opened on May 24, 2024
  1

• representation of a nuc conversion do not point a conversion on the genome

  bug
  nextstrain/ncov#1107 · Filter by author huzuner opened on May 7, 2024
  4

• Add 16 NSPs

  nextstrain/ncov#1081 · Filter by author jameshadfield opened on Aug 21, 2023

• tests/different-inputs.t is outdated and unused

  nextstrain/ncov#1061 · Filter by author victorlin opened on Apr 18, 2023
  1

• can't install to native

  needs information
  nextstrain/ncov#1053 · Filter by author shujiuli opened on Mar 27, 2023
  4

• dev: Document example accepted docker image formats for action

  enhancement
  nextstrain/ncov#1051 · Filter by author corneliusroemer opened on Mar 17, 2023
  2

• after skip_diagnostics: true modification. next strain fails

  bug
  nextstrain/ncov#1035 · Filter by author Valentin-Bio-zz opened on Dec 1, 2022
  3

• Discussion: Do we still need the snp_clusters param for diagnostics rule?

  source: discussion forum
  nextstrain/ncov#1017 · Filter by author joverlee521 opened on Oct 17, 2022
  3

• ENH: Simple reversion coloring to allow inspection of interesting/problematic parts of tree

  enhancement
  nextstrain/ncov#1015 · Filter by author corneliusroemer opened on Oct 14, 2022
  

• ENH: Reconstruct Nextclade Pango Lineage on internal nodes

  enhancement
  nextstrain/ncov#1011 · Filter by author corneliusroemer opened on Oct 6, 2022

• feat: WDL overhaul for Dockstore and Terra

  enhancement
  nextstrain/ncov#1005 · Filter by author j23414 opened on Sep 26, 2022
  

• ENH: Add S1 mutations, reversion count and other branch colorings

  enhancement
  nextstrain/ncov#985 · Filter by author corneliusroemer opened on Jul 24, 2022
  

• Delete pre-computed, downloaded input files on workflow completion on AWS Batch

  nextstrain/ncov#961 · Filter by author tsibley opened on Jun 10, 2022

• Memory resource constraints are not passed to IQ-TREE (via augur tree)

  bug
  nextstrain/ncov#949 · Filter by author AdrianLimaG opened on May 17, 2022
  3

• annotate_metadata_with_index raises ValueError when dtypes don't match

  bugeasy problem
  nextstrain/ncov#948 · Filter by author joverlee521 opened on May 13, 2022
  

• Visualise omicron recombinants

  nextstrain/ncov#915 · Filter by author jameshadfield opened on Apr 13, 2022
  2

• Fetching Open workflow intermediate build assets over S3 gives a 403 error in a really simple setup

  bug
  nextstrain/ncov#909 · Filter by author sacundim opened on Apr 10, 2022
  4