taxonkit

README

TaxonKit - A Cross-platform and Efficient NCBI Taxonomy Toolkit

• Documents: http://bioinf.shenwei.me/taxonkit (Usage, Tutorial)
• Source code: https://github.com/shenwei356/taxonkit
• Latest version:
• Taxid-Changelog: tracking all changes of taxids, including taxids deletion, new adding, merge, reuse, and rank/name changes.
• Please cite:

Subcommands

• list list taxon tree of given taxids
• lineage query lineage of given taxids (supporting STDIN), performance benchmark (details):
• reformat reformat lineage (supporting STDIN)
• name2taxid query taxid by taxon scientific name (supporting STDIN)
• taxid-changelog create taxid changelog from dump archives

Misc

• version print version information and check for update
• genautocomplete generate shell autocompletion script

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 decompress 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 (latest stable version)

brew install brewsci/bio/taxonkit

Method 4: For Go developer (latest stable/dev version)

go get -u github.com/shenwei356/taxonkit/taxonkit

Bash-completion

Note: The current version supports Bash only. This should work for *nix systems with Bash installed.

Howto:

1. run: taxonkit genautocomplete

2. create and edit ~/.bash_completion file if you don't have it.

    nano ~/.bash_completion
   

   add the following:

    for bcfile in ~/.bash_completion.d/* ; do
      . $bcfile
    done
   

Citation

If you use TaxonKit in your work, please cite the preprint.

Contact

Email me for any problem when using taxonkit. shenwei356(at)gmail.com

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

License

MIT License