TaxonKit v0.20.0

Changes

• TaxonKit v0.20.0

  This version is mainly for maintaining compatibility with NCBI's recent changes(1, 2).
  Please remove the ranks.txt file in ~/.taxonkit/ or other directories containing taxdump files (nodes.dmp).

  • taxonkit reformat:
    • Tried to make it compatible with NCBI's recent changes but failed.
    • Update doc to recommend using taxonkit reformat2.
  • taxonkit reformat:
    • Fix handling of deleted TaxIds. #117
    • Change the default output format to be compatible with NCBI's recent changes. #115, #116)
  • taxonkit filter2:
    • Support new ranks: acellular root and cellular root.
      Please remove the ranks.txt file in ~/.taxonkit/ or other directories containing taxdump files (nodes.dmp).
    • Automatically switch on -N/--discard-noranks when only -E/--equal-to is given and the value is not one of ranks without order ("no rank", "clade").
  • taxonkit name2taxid:
    • Remove duplicated records caused by capitalization.

Links

Tips

• run taxonkit version to check update !!!
• run taxonkit genautocomplete to update Bash completion !!!

OS	Arch	File, 中国镜像	Download Count
Linux	64-bit	taxonkit_linux_amd64.tar.gz, 中国镜像
Linux	arm64	taxonkit_linux_arm64.tar.gz, 中国镜像
macOS	64-bit	taxonkit_darwin_amd64.tar.gz, 中国镜像
macOS	arm64	taxonkit_darwin_arm64.tar.gz, 中国镜像
Windows	64-bit	taxonkit_windows_amd64.exe.tar.gz, 中国镜像

Please cite

Shen, W., Ren, H., TaxonKit: a practical and efficient NCBI Taxonomy toolkit,
Journal of Genetics and Genomics, https://doi.org/10.1016/j.jgg.2021.03.006

TaxonKit v0.19.0

Changes

• TaxonKit v0.19.0
  • new command taxonkit reformat2: Reformat lineage in chosen ranks, allowing more ranks than 'reformat'
  • taxonkit reformat:
    • Fix -T/--trim which did not work for -r/--miss-rank-repl. #106

Please cite

Shen, W., Ren, H., TaxonKit: a practical and efficient NCBI Taxonomy toolkit,
Journal of Genetics and Genomics, https://doi.org/10.1016/j.jgg.2021.03.006

TaxonKit v0.18.0

Changes

• TaxonKit v0.18.0
  • taxonkit reformat:
    • Add a placeholder for rank "realm", "{r}", which is common in Virus taxonomy like ictv. #102
  • taxonkit name2taxid:
    • Show warning for names with multiple taxids. #103

TaxonKit v0.17.0

Changes

• TaxonKit v0.17.0
  • taxonkit filter:
    • Fix keeping taxids with a rank of "no rank" or "clade". #97
  • taxonkit list:
    • Accept input TaxIds from stdin/files, not just the flag --ids. #93
  • taxonkit name2taxid:
    • Add support of fuzzy match with -f/--fuzzy. #88
  • taxonkit profile2cami:
    • Add a new flag -S/--no-sum-up to disable summing up abundances. #99

TaxonKit v0.16.0

Changes

• TaxonKit v0.16.0

  • taxonkit create-taxdump:

    • TaxIds are generated from the hash value of "rank+taxon_name", this allowed duplicated names with different ranks (common in GTDB). #92.

  • taxonkit taxid-changelog/create-taxdump:

    • Add notes about the possible error records in taxid-changelog built from taxonomic data created by create-taxdump. #91

    • Dont't worry, a single version of taxonomic data created by taxonkit create-taxdump has no problem, it's just the changelog might not be perfect.

      $ taxonkit taxid-changelog -h
      Create TaxId changelog from dump archives
      
      Attention:
        1. This command was originally designed for NCBI taxonomy, where the the TaxIds are stable.
        2. For other taxonomic data created by "taxonkit create-taxdump", e.g., GTDB-taxdump,
          some change events might be wrong, because
           a) There would be dramatic changes between the two versions.
           b) Different taxons in multiple versions might have the same TaxIds, because we only
              check and eliminate taxid collision within a single version.
           So a single version of taxonomic data created by "taxonkit create-taxdump" has no problem,
           it's just the changelog might not be perfect.
      
      $ taxonkit create-taxdump -h
      Attention:
        3. We only check and eliminate taxid collision within a single version of taxonomy data.
           Therefore, if you create taxid-changelog with "taxid-changelog", different taxons
           in multiple versions might have the same TaxIds and some change events might be wrong.
      
           So a single version of taxonomic data created by "taxonkit create-taxdump" has no problem,
           it's just the changelog might not be perfect.
      

  • taxonkit lca:

    • new flag -K/--keep-invalid: print the query even if no single valid taxid left. #89

Please cite

Shen, W., Ren, H., TaxonKit: a practical and efficient NCBI Taxonomy toolkit,
Journal of Genetics and Genomics, https://doi.org/10.1016/j.jgg.2021.03.006

TaxonKit v0.15.1

Changes

• TaxonKit v0.15.1
  • taxonkit name2taxid:
    • remove the restriction of name types. #87
  • added a new tutorual: Mapping old species names to new ones.

Please cite

Shen, W., Ren, H., TaxonKit: a practical and efficient NCBI Taxonomy toolkit,
Journal of Genetics and Genomics, https://doi.org/10.1016/j.jgg.2021.03.006

Links

Tips

• run taxonkit version to check update !!!
• run taxonkit genautocomplete to update Bash completion !!!

OS	Arch	File, 中国镜像	Download Count
Linux	64-bit	taxonkit_linux_amd64.tar.gz, 中国镜像
Linux	arm64	taxonkit_linux_arm64.tar.gz, 中国镜像
macOS	64-bit	taxonkit_darwin_amd64.tar.gz, 中国镜像
macOS	arm64	taxonkit_darwin_arm64.tar.gz, 中国镜像
Windows	64-bit	taxonkit_windows_amd64.exe.tar.gz, 中国镜像

TaxonKit v0.15.0

Changes

• TaxonKit v0.15.0
  • taxonkit reformat:
    • For lineages with more than one node, if it fails to query TaxId with the parent-child pair, use the last child only. #82
    • The flag -T/--trim also does not add the prefix for missing ranks lower than the current rank. #82
    • New flag -s/--miss-rank-repl-suffix to set the suffix for estimated taxon names. #85

TaxonKit v0.14.2

Changes

• TaxonKit v0.14.2
  • taxonkit filter:
    • fix checking merged/deleted/not-found taxids. #80
  • taxonkit lca:
    • add a new flag -b/--buffer-size to set the size of the line buffer. #75
    • fix typos: --separater -> --separater, the former is still available for backward compatibility.
  • taxonkit reformat:
    • output compatible format for TaxIds not found in the database. #79
  • taxonkit taxid-changelog:
    • support gzip-compressed taxdump files for saving space. #78

TaxonKit v0.14.1

Changes

• TaxonKit v0.14.1
  • taxonkit reformat:
    • The flag -S/--pseudo-strain does not require -F/--fill-miss-rank now.
    • For taxa of rank >= species, {t}, {S}, and T outputs nothing when using -S/--pseudo-strain.

TaxonKit v0.14.0

Changes

• TaxonKit v0.14.0
  • taxonkit create-taxdump:
    • save taxIds in int32 instead of uint32, as BLAST and DIAMOND do. #70
  • taxonkit list:
    • do not skip visited subtrees when some of the given taxids are descendants of others. #68
  • taxonkit:
    • when environment variable TAXONKIT_DB is set, explicitly setting --data-dir will override the value of TAXONKIT_DB.