TaxonKit - A Practical and Efficient NCBI Taxonomy ToolkitLink

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)

FeaturesLink

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

SubcommandsLink

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 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.

taxonkit

BenchmarkLink

Getting complete lineage for given TaxIds

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

DatasetLink

Download and uncompress taxdump.tar.gz: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
Copy names.dmp, nodes.dmp, delnodes.dmp and merged.dmp to data directory: $HOME/.taxonkit, e.g., /home/shenwei/.taxonkit ,
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.

InstallationLink

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)Link

Just download compressed executable file of your operating system, and uncompress it with tar -zxvf *.tar.gz command or other tools. And then:

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

Method 2: Install via conda (latest stable version) Link

conda install -c bioconda taxonkit

Method 3: Install via homebrew (out of date)Link

brew install brewsci/bio/taxonkit

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

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

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-completionLink

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

CitationLink

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

ContactLink

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

LicenseLink

MIT License

StarchartLink

Stargazers over time