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