taxonkit

README

TaxonKit - A Cross-platform and Efficient NCBI Taxonomy Toolkit

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

Table of Contents

• Features
• Subcommands
• Benchmark
• Dataset
• Installation
• Bash-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, phylum, class, order, family, genus, species"
  • Featured command: filtering taxiDs by rank range, e.g., genus or lower ranks.

Subcommands

Subcommand	Function
list	List taxonomic subtrees (taxIDs) bellow given taxIDs
lineage	Query taxonomic lineage of given taxIDs
reformat	Reformat lineage in canonical ranks
name2taxid	Convert scientific 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
version	Print version information and check for update
genautocomplete	Generate shell autocompletion script

Benchmark

1. Getting full lineage for given taxIDs

   

Dataset

1. Download and decompress 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

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

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

License

MIT License

Starchart