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• Documents:https://bioinf.shenwei.me/taxonkit(Usage&Examples,Tutorial,中文介绍)
• Source code:https://github.com/shenwei356/taxonkit
• Latest version:
• Please cite:https://doi.org/10.1016/j.jgg.2021.03.006
• pytaxonkit, Python bindings for TaxonKit.

Related projects:

• Taxid-Changelog: Tracking all changes of TaxIds, including deletion, new adding, merge, reuse, and rank/name changes.
• GTDB taxdump: GTDB taxonomy taxdump files with trackable TaxIds.
• ICTV taxdump: NCBI-style taxdump files for International Committee on Taxonomy of Viruses (ICTV)

• Features
• Subcommands
• Benchmark
• Dataset
• Installation
• Command-line completion
• Citation
• Contact
• License

• Easy to install (download)
  • Statically linked executable binaries for multiple platforms (Linux/Windows/macOS, amd64/arm64)
  • Light weight and out-of-the-box, no dependencies, no compilation, no configuration
  • No database building, just downloadNCBI taxonomy data and uncompress to$HOME/.taxonkit
• Easy to use (usages and examples)
  • Supportingbash-completion
  • Fast (seebenchmark), multiple-CPUs supported, most operations cost 2-10s.
  • Detailed usages and examples
  • Supporting STDIN and (gzipped) input/output file, easily integrated in pipe
• Versatile commands
  • Usage and examples
  • Featured command:tracking monthly changelog of all TaxIds
  • Featured command:reformating lineage into format of seven-level ("superkingdom/kingdom, phylum, class, order, family, genus, species", andeven all possible ranks
  • Featured command:filtering taxiDs by a rank range, e.g., at or below genus rank.
  • Featured command:Create NCBI-style taxdump files for custom taxonomy, e.g., GTDB and ICTV

Note:^*New commands since the publication.

1. Getting complete lineage for given TaxIds (this plot is very old).

   

   Versions: ETE=3.1.2, taxopy=0.5.0 (faster since 0.6.0), TaxonKit=0.7.2.

1. Download and uncompresstaxdump.tar.gz:https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
2. Copynames.dmp,nodes.dmp,delnodes.dmp andmerged.dmp to data directory:$HOME/.taxonkit,e.g.,/home/shenwei/.taxonkit ,
3. Optionally copy to some other directories, and later you can refer to using flag--data-dir,or environment variableTAXONKIT_DB.

All-in-one command:

wget -c https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz tar -zxvf taxdump.tar.gzmkdir -p $HOME/.taxonkitcp names.dmp nodes.dmp delnodes.dmp merged.dmp $HOME/.taxonkit

Update dataset: Simply re-download the taxdump files, uncompress and override old ones.

Go toDownload Page for more download options and changelogs.

TaxonKit is implemented inGo programming language,executable binary filesfor most popular operating systems are freely availableinrelease page.

Justdownload compressedexecutable file of your operating system,and uncompress it withtar -zxvf *.tar.gz command or other tools.And then:

1. For Linux-like systems

   1. If you have root privilege simply copy it to/usr/local/bin:

       sudo cp taxonkit /usr/local/bin/

   2. Or copy to anywhere in the environment variablePATH:

       mkdir -p $HOME/bin/; cp taxonkit $HOME/bin/

2. For Windows, just copytaxonkit.exe toC:\WINDOWS\system32.

conda install -c bioconda taxonkit

brew install brewsci/bio/taxonkit

1. Install go

    wget https://go.dev/dl/go1.24.1.linux-amd64.tar.gz tar -zxf go1.24.1.linux-amd64.tar.gz -C $HOME/ # or  #   echo "export PATH=$PATH:$HOME/go/bin" >> ~/.bashrc #   source ~/.bashrc export PATH=$PATH:$HOME/go/bin

2. Compile TaxonKit

    # ------------- the latest stable version ------------- go get -v -u github.com/shenwei356/taxonkit/taxonkit # The executable binary file is located in: #   ~/go/bin/taxonkit # You can also move it to anywhere in the $PATH mkdir -p $HOME/bin cp ~/go/bin/taxonkit $HOME/bin/ # --------------- the development version -------------- git clone https://github.com/shenwei356/taxonkit cd taxonkit/taxonkit/ go build # The executable binary file is located in: #   ./taxonkit # You can also move it to anywhere in the $PATH mkdir -p $HOME/bin cp ./taxonkit $HOME/bin/

Supported shell: bash|zsh|fish|powershell

Bash:

# generate completion shelltaxonkit genautocomplete --shell bash# configure if never did.# install bash-completion if the "complete" command is not found.echo "for bcfile in ~/.bash_completion.d/* ; do source \$bcfile; done" >> ~/.bash_completionecho "source ~/.bash_completion" >> ~/.bashrc

Zsh:

# generate completion shelltaxonkit genautocomplete --shell zsh --file ~/.zfunc/_taxonkit# configure if never didecho 'fpath=( ~/.zfunc "${fpath[@]}" )' >> ~/.zshrcecho "autoload -U compinit; compinit" >> ~/.zshrc

fish:

taxonkit genautocomplete --shell fish --file ~/.config/fish/completions/taxonkit.fish

If you use TaxonKit in your work, 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

Create an issue to report bugs,propose new functions or ask for help.

MIT License