nextstrain/nextclade

Issues

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

  #1552 opened a month ago by jurresiegers
  9

• Run `sort` command without pre-calculated minimizer index

  #1554 opened a month ago by ivan-aksamentov
  0

• In web GUI when clicking on tree, getting "Type Error: undefined is not an iterable"

  #1547 opened 2 months ago by corneliusroemer
  7

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

  #1545 opened 2 months ago by ammaraziz
  2

• Assigned Clade different from Clade of assigned node

  #1525 opened 3 months ago by taeschbacher-gilead
  3

• Synonymous mutations

  #1535 opened 2 months ago by claudia-as
  1

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

  #1537 opened 2 months ago by corneliusroemer
  3

• CI is broken

  #1532 opened 2 months ago by ivan-aksamentov
  2

• qc algorithm for nonACTGNs

  #1524 opened 3 months ago by ryhisner
  2

• Definition of Private Mutation/Deletion in Nextclade CLI ndjson

  #1523 opened 3 months ago by ryhisner
  2

• nextclade run with optional dataset tag input

  #1521 opened 4 months ago by jrotieno
  5

• Nucleotide insertions not shown in peptide tooltip, causing confusion in case of frameshift due to nt insertion

  #1520 opened 4 months ago by whottel
  6

• Can't do quality control when change reference

  #1519 opened 4 months ago by YangJingqii
  1

• List of mutational changes per clade

  #1515 opened 5 months ago by huzuner
  2

• Can influenza H5 datasets be available for nextclade CLI

  #1516 opened 5 months ago by molly-hetheringtonrauth
  3

• Add coverage per CDS to output

  #1513 opened 5 months ago by joverlee521
  8

• Default threads for webapp are set too high

  #1511 opened 6 months ago by corneliusroemer
  2

• SVG download for the Results table

  #1510 opened 6 months ago by joverlee521
  0

• Bioconda workflow failed with push error due to insufficient permissions

  #1509 opened 6 months ago by corneliusroemer
  7

• How does one update Nextclade CLI? I cannot find any instructions on the Nextclade CLI page, only descriptions of various updates?

  #1506 opened 6 months ago by ryhisner
  1

• Frameshift and insertion markers cannot be disabled/configured in contrast to all other markers

  #1477 opened 6 months ago by corneliusroemer
  0

• Unfolding <details> in changelog in website jumbles things up

  #1487 opened 6 months ago by corneliusroemer
  0

• Rename `master` to `main`

  #1488 opened 6 months ago by genehack
  0

• Max marker setting even counts markers that are off

  #1476 opened 7 months ago by corneliusroemer
  0

• [minor] Auspice dataset functionality: URL redirects don't update displayed metadata

  #1475 opened 7 months ago by jameshadfield
  3

• nextclade run --output-columns-selection throws error for seqName and includes index even though I don't want index

  #1459 opened 7 months ago by AngieHinrichs
  11

• ENH(nextclade cli): nextclade dataset list: indicate whether clades can be assigned

  #1458 opened 7 months ago by AngieHinrichs
  7

• Nextclade Web: don't store unnecessary dataset info in local storage

  #1464 opened 7 months ago by ivan-aksamentov
  0

• Nextclade Web: Confusing unwanted dataset switching

  #1462 opened 7 months ago by ivan-aksamentov
  3

• Nextclade Web: consider rethinking dataset badges

  #1463 opened 7 months ago by ivan-aksamentov
  1

• docs: document nextalign-like use-case

  #1456 opened 7 months ago by ivan-aksamentov
  1

• Community build cache validity bug

  #1450 opened 7 months ago by jameshadfield
  2

• Scrollbar shown for dataset names in dataset picker

  #1437 opened 7 months ago by corneliusroemer
  9

• How to get the latest Lineage- with CLI

  #1449 opened 7 months ago by kiranpatil222
  4

• Developer guide uses deprecated CLI option

  #1451 opened 8 months ago by genehack
  0

• Add a BA.1 reference for the web nextclade version

  #1426 opened 10 months ago by murallcl
  4

• Update Fred Hutch logo

  #1447 opened 8 months ago by genehack
  0

• --input-dataset parameter

  #1445 opened 8 months ago by AJFeng
  5

• output TSV column(s) for missing bases at beginning and end of sequence?

  #1443 opened 8 months ago by AngieHinrichs
  1

• how to generate the result table by the cli version auspice

  #1441 opened 8 months ago by baimianer
  4

• When using `?input-fasta=` url query param without specifying dataset, web auto-starts analysis (prematurely)

  #1436 opened 8 months ago by corneliusroemer
  5

• `--input-pcr-primers` listed in CLI help options despite being removed in v3

  #1432 opened 9 months ago by kapsakcj
  2

• 21L Tree Updates?

  #1431 opened 9 months ago by ryhisner
  2

• Beginners Help with Nextclade CLI

  #1416 opened 10 months ago by ryhisner
  6

• Feature Request: Dataset download all datasets within specified path

  #1410 opened a year ago by ammaraziz
  4

• Erroneous Clade Assignment or More Refined Tool?

  #1425 opened 10 months ago by coreymeloche
  4

• error when using `nextclade dataset get --verbosity` flag

  #1428 opened 10 months ago by kapsakcj
  3

• Empty input file causes uncaught error in v3 (it didn't in v2)

  #1422 opened 10 months ago by corneliusroemer
  0

• Can support be extended for SC2 Datasets V2 for another month?

  #1397 opened 10 months ago by ammaraziz
  4

• 3.0.0 version not retrieving RSV datasets

  #1391 opened a year ago by ric-costa
  1