TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit

• 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)

Table of Contents

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

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Features

• 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 download NCBI taxonomy data and uncompress to $HOME/.taxonkit
• Easy to use (usages and examples)
  • Supporting bash-completion
  • Fast (see benchmark), 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", and even 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

Subcommands

Subcommand |Function :-----------------------------------------------------------------------------|:---------------------------------------------- list |List taxonomic subtrees (TaxIds) bellow given TaxIds lineage |Query taxonomic lineage of given TaxIds reformat |Reformat lineage in canonical ranks reformat2|Reformat lineage in chosen ranks, allowing more ranks than 'reformat' name2taxid |Convert taxon names to TaxIds filter |Filter TaxIds by taxonomic rank range lca |Compute lowest common ancestor (LCA) for TaxIds taxid-changelog|Create TaxId changelog from dump archives profile2cami |Convert metagenomic profile table to CAMI format cami-filter |Remove taxa of given TaxIds and their descendants in CAMI metagenomic profile create-taxdump |Create NCBI-style taxdump files for custom taxonomy, e.g., GTDB and ICTV

Note: ^*New commands since the publication.

<img src="taxonkit.jpg" alt="taxonkit" width="700" align="center" />

Benchmark

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

   <img src="bench/bench.get_lineage.reformat.tsv.png" alt="" width="600" align="center" />

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

Dataset

1. Download and uncompress taxdump.tar.gz: https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
2. Copy names.dmp, nodes.dmp, delnodes.dmp and merged.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 variable TAXONKIT_DB.

All-in-one command:

wget -c https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz 
tar -zxvf taxdump.tar.gz

mkdir -p $HOME/.taxonkit
cp names.dmp nodes.dmp delnodes.dmp merged.dmp $HOME/.taxonkit

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

Installation

Go to Download Page for more download options and changelogs.

TaxonKit is implemented in Go programming language, executable binary files for most popular operating systems are freely available in release page.

Method 1: Download binaries (latest stable/dev version)

Just download compressed executable file of your operating system, and uncompress it with tar -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 variable PATH:

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

2. For Windows, just copy taxonkit.exe to C:\WINDOWS\system32.

Method 2: Install via conda (latest stable version)

conda install -c bioconda taxonkit

Method 3: Install via homebrew (out of date)

brew install brewsci/bio/taxonkit

Method 4: Compile from source (latest stable/dev version)

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/
   

Bash-completion

Supported shell: bash|zsh|fish|powershell

Bash:

# generate completion shell
taxonkit gena