README.md

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

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

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"
  • 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.

Benchmark

1. Getting complete lineage for given TaxIds

   

   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: ftp://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 ftp://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/go1.17.13.linux-amd64.tar.gz
   
    tar -zxf go1.17.13.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 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_completion
echo "source ~/.bash_completion" >> ~/.bashrc

Zsh:

# generate completion shell
taxonkit genautocomplete --shell zsh --file ~/.zfunc/_taxonkit

# configure if never did
echo 'fpath=( ~/.zfunc "${fpath[@]}" )' >> ~/.zshrc
echo "autoload -U compinit; compinit" >> ~/.zshrc

fish:

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

Citation

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

Contact

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

License

MIT License

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