FOI-Bioinformatics/flextaxd

Issues

• Question about assembly level in creating flextaxd database

  #71 opened a month ago by ingridvanw
  0

• flextaxd error: "ValueError: not enough values to unpack (expected 2, got 1)"

  #70 opened 9 months ago by morien
  2

• [Question] Does taxonomy exported from flextaxd only contained species with genome available in refseq folder? Can I make use of library.fna downloaded via kraken2-build?

  #56 opened 2 years ago by zztin
  0

• Adding a custom seqid2taxid file to the NCBI accession2taxid causes error

  #55 opened 2 years ago by MortenEneberg
  1

• Flextaxd creates empty kraken db

  #48 opened 2 years ago by SilasK
  14

• Create completely custom Kraken2 database

  #51 opened 2 years ago by mw55309
  5

• Self linked parents

  #37 opened 2 years ago by davve2
  0

• Use of custom genomes retrieved from another databases apart from NCBI and GTDB in FlexTaxD

  #52 opened 2 years ago by magibc
  5

• Building Kraken2 compatible GTDB only database

  #33 opened 4 years ago by HitMonk
  35

• Krakenuniq "Unknown options: skip-maps"

  #50 opened 3 years ago by MortenEneberg
  2

• Flextaxd - test database inspect file has no genome names

  #49 opened 3 years ago by MortenEneberg
  13

• Issues with replacing NCBI bacterial and archeal taxonomies with GTDB taxonomies

  #47 opened 3 years ago by MortenEneberg
  11

• TypeError: 'int' object is not iterable

  #46 opened 3 years ago by xvtyzn
  3

• Citation

  #19 opened 4 years ago by Midnighter
  3

• MP style output

  #45 opened 3 years ago by davve2
  1

• Issues with cleaning and merging NCBI+GTDB database

  #44 opened 3 years ago by HitMonk
  3

• 16s GTDB database: Kingdom taxonomy issue

  #41 opened 3 years ago by HitMonk
  3

• Error message when no gneomes are found

  #36 opened 4 years ago by SilasK
  1

• Importing trees with unspecified rank levels

  #38 opened 4 years ago by davve2
  0

• Using flextaxd to modify the taxonomy without genomes

  #35 opened 4 years ago by mw55309
  3

• Custom genome annotations with "-" sometimes gets lost

  #34 opened 4 years ago by davve2
  0

• Bug on replace

  #31 opened 4 years ago by davve2
  1

• Use GTDB genomes (representatives or all) instead of NCBI

  #28 opened 4 years ago by davve2
  0

• Cano not import name "BadGzipFile"

  #29 opened 4 years ago by alienzj
  3

• flextaxd-create doesn't find custum genomes.

  #16 opened 4 years ago by SilasK
  24

• genomeid2taxid of local files does not allow names to be without .fa/.fasta

  #24 opened 4 years ago by davve2
  0

• Add - to fit bracken names and nodes format

  #25 opened 4 years ago by davve2
  1

• Non-unique contig names for GTDB

  #22 opened 4 years ago by andrewjmc
  5

• Additional advice/walkthrough

  #17 opened 4 years ago by andrewjmc
  12

• Duplicated parents?

  #20 opened 4 years ago by davve2
  5

• Empty folder are downloaded

  #10 opened 4 years ago by davve2
  0

• Referenced genomes remain even if node is updated (on replace)

  #8 opened 4 years ago by davve2
  0

• Not all superkingdoms appear in nodes.dmp file

  #12 opened 4 years ago by punnettsun
  1

• flextaxd strain rank?

  #11 opened 4 years ago by punnettsun
  4

• pip install fails in Ubuntu 16.04

  #1 opened 5 years ago by tolot27
  1

• conda installation fails

  #2 opened 5 years ago by tolot27
  1