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https://github.com/shenwei356/taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
https://github.com/shenwei356/taxonkit

bioinformatics cross-platform lca lineage taxdump taxid taxonkit taxonomy

Last synced: about 2 months ago
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A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

Host: GitHub
URL: https://github.com/shenwei356/taxonkit
Owner: shenwei356
License: mit
Created: 2016-11-01T16:02:46.000Z (almost 8 years ago)
Default Branch: master
Last Pushed: 2024-06-23T10:10:28.000Z (3 months ago)
Last Synced: 2024-06-23T11:26:23.124Z (3 months ago)
Topics: bioinformatics, cross-platform, lca, lineage, taxdump, taxid, taxonkit, taxonomy
Language: Go
Homepage: https://bioinf.shenwei.me/taxonkit
Size: 14.2 MB
Stars: 348
Watchers: 10
Forks: 29
Open Issues: 10
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE

Awesome Lists containing this project

awesome-bio-go - taxonkit
top-life-sciences - **shenwei356/taxonkit** - style taxdump files for custom taxonomies like GTDB/ICTV<br>`bioinformatics`, `cross-platform`, `lca`, `lineage`, `taxdump`, `taxid`, `taxonkit`, `taxonomy`<br><img src='https://github.com/HubTou/topgh/blob/main/icons/gstars.png'> 342 <img src='https://github.com/HubTou/topgh/blob/main/icons/forks.png'> 29 <img src='https://github.com/HubTou/topgh/blob/main/icons/watchers.png'> 10 <img src='https://github.com/HubTou/topgh/blob/main/icons/code.png'> Go <img src='https://github.com/HubTou/topgh/blob/main/icons/license.png'> MIT license <img src='https://github.com/HubTou/topgh/blob/main/icons/last.png'> 2024-04-25 17:15:34 | (Ranked by starred repositories)

README

        # TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit

- **Documents:** [https://bioinf.shenwei.me/taxonkit](https://bioinf.shenwei.me/taxonkit)

([**Usage&Examples**](https://bioinf.shenwei.me/taxonkit/usage/),

[**Tutorial**](https://bioinf.shenwei.me/taxonkit/tutorial/), [**中文介绍**](https://bioinf.shenwei.me/taxonkit/chinese/))

- **Source code:** [https://github.com/shenwei356/taxonkit](https://github.com/shenwei356/taxonkit)

[![GitHub stars](https://img.shields.io/github/stars/shenwei356/taxonkit.svg?style=social&label=Star&?maxAge=2592000)](https://github.com/shenwei356/taxonkit)

[![license](https://img.shields.io/github/license/shenwei356/taxonkit.svg?maxAge=2592000)](https://github.com/shenwei356/taxonkit/blob/master/LICENSE)

[![Built with GoLang](https://img.shields.io/badge/powered_by-go-6362c2.svg?style=flat)](https://golang.org)

- **Latest version:** [![Latest Version](https://img.shields.io/github/release/shenwei356/taxonkit.svg?style=flat?maxAge=86400)](https://github.com/shenwei356/taxonkit/releases)

[![Github Releases](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/total.svg?maxAge=3600)](https://bioinf.shenwei.me/taxonkit/download/)

[![Cross-platform](https://img.shields.io/badge/platform-any-ec2eb4.svg?style=flat)](https://bioinf.shenwei.me/taxonkit/download/)

[![Anaconda Cloud](	https://anaconda.org/bioconda/taxonkit/badges/version.svg)](https://anaconda.org/bioconda/taxonkit)

- **[Please cite](#citation):** [https://doi.org/10.1016/j.jgg.2021.03.006](https://www.sciencedirect.com/science/article/pii/S1673852721000837)

[![Citation Badge](https://api.juleskreuer.eu/citation-badge.php?doi=10.1016/j.jgg.2021.03.006)](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=wHF3Lm8AAAAJ&citation_for_view=wHF3Lm8AAAAJ:ULOm3_A8WrAC)

- [pytaxonkit](https://github.com/bioforensics/pytaxonkit), Python bindings for TaxonKit.

Related projects:

- [**Taxid-Changelog**](https://github.com/shenwei356/taxid-changelog): Tracking all changes of TaxIds, including deletion, new adding, merge, reuse, and rank/name changes.

- [GTDB taxdump](https://github.com/shenwei356/gtdb-taxdump): GTDB taxonomy taxdump files with trackable TaxIds.

- [ICTV taxdump](https://github.com/shenwei356/ictv-taxdump): NCBI-style taxdump files for International Committee on Taxonomy of Viruses (ICTV)

## Table of Contents

- [Features](#features)

- [Subcommands](#subcommands)

- [Benchmark](#benchmark)

- [Dataset](#dataset)

- [Installation](#installation)

- [Command-line completion](#command-line-completion)

- [Citation](#citation)

- [Contact](#contact)

- [License](#license)

## Features

- **Easy to install** ([download](http://bioinf.shenwei.me/taxonkit/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](https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz) and uncompress to `$HOME/.taxonkit`

- **Easy to use** ([usages and examples](http://bioinf.shenwei.me/taxonkit/usage/))

    - Supporting [bash-completion](#bash-completion)

    - Fast (see [benchmark](#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](http://bioinf.shenwei.me/taxonkit/usage/)

    - Featured command: [tracking monthly changelog of all TaxIds](https://github.com/shenwei356/taxid-changelog)

    - Featured command: [reformating lineage into format of seven-level ("superkingdom/kingdom, phylum, class, order, family, genus, species"](https://bioinf.shenwei.me/taxonkit/usage/#reformat)

    - Featured command: [filtering taxiDs by a rank range](http://bioinf.shenwei.me/taxonkit/usage/#filter), e.g., at or below genus rank.

    - Featured command: [**Create NCBI-style taxdump files for custom taxonomy, e.g., GTDB and ICTV**](https://bioinf.shenwei.me/taxonkit/usage/#create-taxdump)

## Subcommands

Subcommand                                                                    |Function

:-----------------------------------------------------------------------------|:----------------------------------------------

[`list`](https://bioinf.shenwei.me/taxonkit/usage/#list)                      |List taxonomic subtrees (TaxIds) bellow given TaxIds

[`lineage`](https://bioinf.shenwei.me/taxonkit/usage/#lineage)                |Query taxonomic lineage of given TaxIds

[`reformat`](https://bioinf.shenwei.me/taxonkit/usage/#reformat)              |Reformat lineage in canonical ranks

[`name2taxid`](https://bioinf.shenwei.me/taxonkit/usage/#name2taxid)          |Convert taxon names to TaxIds

[`filter`](https://bioinf.shenwei.me/taxonkit/usage/#filter)                  |Filter TaxIds by taxonomic rank range

[`lca`](https://bioinf.shenwei.me/taxonkit/usage/#lca)                        |Compute lowest common ancestor (LCA) for TaxIds

[`taxid-changelog`](https://bioinf.shenwei.me/taxonkit/usage/#taxid-changelog)|Create TaxId changelog from dump archives

[`profile2cami`](https://bioinf.shenwei.me/taxonkit/usage/#profile2cami)^*     |Convert metagenomic profile table to CAMI format 

[`cami-filter`](https://bioinf.shenwei.me/taxonkit/usage/#cami-filter)^*        |Remove taxa of given TaxIds and their descendants in CAMI metagenomic profile

[`create-taxdump`](https://bioinf.shenwei.me/taxonkit/usage/#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](https://github.com/shenwei356/taxonkit/issues/47)), 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](https://bioinf.shenwei.me/taxonkit/download) for more download options and changelogs.

`TaxonKit` is implemented in [Go](https://golang.org/) programming language,

 executable binary files **for most popular operating systems** are freely available

  in [release](https://github.com/shenwei356/taxonkit/releases) page.

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

Just [download](https://github.com/shenwei356/taxonkit/releases) 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/

    1. Or copy to anywhere in the environment variable `PATH`:

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

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

#### Method 2: Install via conda  (latest stable version) [![Install-with-conda](https://anaconda.org/bioconda/taxonkit/badges/installer/conda.svg)](https://bioinf.shenwei.me/taxonkit/download/) [![Anaconda Cloud](https://anaconda.org/bioconda/taxonkit/badges/version.svg)](https://anaconda.org/bioconda/taxonkit) [![downloads](https://anaconda.org/bioconda/taxonkit/badges/downloads.svg)](https://anaconda.org/bioconda/taxonkit)

    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](https://go.dev/doc/install)

        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](https://www.sciencedirect.com/science/article/pii/S1673852721000837) [![Citation Badge](https://api.juleskreuer.eu/citation-badge.php?doi=10.1016/j.jgg.2021.03.006)](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=wHF3Lm8AAAAJ&citation_for_view=wHF3Lm8AAAAJ:ULOm3_A8WrAC)

## Contact

[Create an issue](https://github.com/shenwei356/taxonkit/issues) to report bugs,

propose new functions or ask for help.

## License

[MIT License](https://github.com/shenwei356/taxonkit/blob/master/LICENSE)

## Starchart