Issues

• Add HMM-based recombination detection

  t:feat
  Feature

  nextstrain/nextclade#1768 · Filter by author nneune opened on Jun 29, 2026
  1

• error when choose reference Mpox cladeI

  t:bug
  nextstrain/nextclade#1766 · Filter by author celyfoudalnsp opened on Apr 29, 2026
  6

• Searching for datasets scrolls confusingly

  t:bug
  nextstrain/nextclade#1746 · Filter by author theosanderson opened on Feb 4, 2026
  3

• Schema validation for pathogen.json does not reject unknown fields or catch typos

  bug
  nextstrain/nextclade#1711 · Filter by author nneune opened on Dec 8, 2025
  6

• QC label for recombinant sequences

  t:feat
  nextstrain/nextclade#1699 · Filter by author nneune opened on Oct 17, 2025
  5

• npm package for nextclade in WASM

  t:feat
  nextstrain/nextclade#1685 · Filter by author theosanderson opened on Sep 29, 2025
  4

• Incorrect placement of ORF9b amino acid substitution adjacent to a deletion (lineage XFC.1)

  t:bug
  nextstrain/nextclade#1670 · Filter by author LucvZon opened on Aug 12, 2025
  3

• potential bug: band boundary hit when trailing in-dels are present at the end of a simple stripe alignment

  needs triaget:bug
  nextstrain/nextclade#1654 · Filter by author mmolari opened on Jun 26, 2025
  1

• "Error: Internal Error: Dataset not found: 'http://localhost:3000'."

  needs triaget:bug
  nextstrain/nextclade#1653 · Filter by author corneliusroemer opened on Jun 20, 2025

• "Range Error: Invalid string length" in JS when launching web worker

  s:nextclade_webt:bug
  nextstrain/nextclade#1651 · Filter by author corneliusroemer opened on Jun 15, 2025

• bzip2 has a native Rust implementation

  t:feat
  nextstrain/nextclade#1650 · Filter by author fanninpm opened on Jun 13, 2025
  1

• Suggestion crashes with OOM from around ~3k HA seqs (6MB)

  package: nextclade_webt:bug
  nextstrain/nextclade#1647 · Filter by author corneliusroemer opened on Jun 7, 2025
  1

• nextclade --help --color=never still gives colorized output

  t:bug
  nextstrain/nextclade#1629 · Filter by author ivan-aksamentov opened on May 23, 2025
  1

• Different CLI outputs with nextclade and nextclade --verbose

  t:bug
  nextstrain/nextclade#1627 · Filter by author ivan-aksamentov opened on May 22, 2025

• Identical Sequences Assigned to Different Branches

  t:bug
  nextstrain/nextclade#1595 · Filter by author RanWei1987 opened on Mar 26, 2025
  1

• Unexpected behavior: Nextclade ignores CDS unlinked to gene if gene is in gff3

  nextstrain/nextclade#1576 · Filter by author anna-parker opened on Feb 28, 2025
  3

• Difference between Nextclade and standard variant calling process

  t:ask
  nextstrain/nextclade#1575 · Filter by author potatolover222 opened on Feb 25, 2025
  5

• Do something other than just crashing when people upload too many sequences for Nextclade

  package: nextclade_webt:bug
  nextstrain/nextclade#1570 · Filter by author corneliusroemer opened on Feb 21, 2025
  2

• Run sort command without pre-calculated minimizer index

  package: nextclade_clipackage: nextcladet:feat
  nextstrain/nextclade#1554 · Filter by author ivan-aksamentov opened on Nov 20, 2024

• H9Nx (all lineages), H9Nx (Y-lineage), H9Nx (G-lineage), H9Nx (B-lineage)

  t:feat
  nextstrain/nextclade#1552 · Filter by author jurresiegers opened on Nov 18, 2024
  9

• Feature Request: More categories for '--output-columns-selection'

  t:feat
  nextstrain/nextclade#1545 · Filter by author ammaraziz opened on Nov 5, 2024
  2

• Allow toggling of sort state by clicking on column name/text itself

  package: nextclade_webt:feat
  nextstrain/nextclade#1537 · Filter by author corneliusroemer opened on Oct 16, 2024
  3

• Synonymous mutations

  nextstrain/nextclade#1535 · Filter by author claudia-as opened on Oct 16, 2024
  1

• Definition of Private Mutation/Deletion in Nextclade CLI ndjson

  needs triaget:ask
  nextstrain/nextclade#1523 · Filter by author ryhisner opened on Sep 14, 2024
  2

• nextclade run with optional dataset tag input

  t:feat
  nextstrain/nextclade#1521 · Filter by author jrotieno opened on Sep 11, 2024
  5