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TaxonKit is implemented in Go programming language, executable binary files for most popular operating systems are freely available in release page.

Current Version

• TaxonKit v0.14.2
  • taxonkit filter:
    • fix checking merged/deleted/not-found taxids. #80
  • taxonkit lca:
    • add a new flag -b/--buffer-size to set the size of the line buffer. #75
    • fix typos: --separater -> --separater, the former is still available for backward compatibility.
  • taxonkit reformat:
    • output compatible format for TaxIds not found in the database. #79
  • taxonkit taxid-changelog:
    • support gzip-compressed taxdump files for saving space. #78

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

Links

Tips

• run taxonkit version to check update !!!
• run taxonkit genautocomplete to update Bash completion !!!

OS	Arch	File, 中国镜像	Download Count
Linux	64-bit	taxonkit_linux_amd64.tar.gz, 中国镜像
Linux	arm64	taxonkit_linux_arm64.tar.gz, 中国镜像
macOS	64-bit	taxonkit_darwin_amd64.tar.gz, 中国镜像
macOS	arm64	taxonkit_darwin_arm64.tar.gz, 中国镜像
Windows	64-bit	taxonkit_windows_amd64.exe.tar.gz, 中国镜像

Installation

Download Page

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 (may not the lastest version)

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

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.

Release history

• TaxonKit v0.14.1
  • taxonkit reformat:
    • The flag -S/--pseudo-strain does not require -F/--fill-miss-rank now.
    • For taxa of rank >= species, {t}, {S}, and T outputs nothing when using -S/--pseudo-strain.
• TaxonKit v0.14.0
  • taxonkit create-taxdump:
    • save taxIds in int32 instead of uint32, as BLAST and DIAMOND do. #70
  • taxonkit list:
    • do not skip visited subtrees when some of give taxids are descendants of others. #68
  • taxonkit:
    • when environment variable TAXONKIT_DB is set, explicitly setting --data-dir will override the value of TAXONKIT_DB.
• TaxonKit v0.13.0
  • taxonkit reformat:
    • add a new placeholder {K} for rank kingdom. #64
    • do not panic for invalid TaxIds, e.g., the column name, when using -I--taxid-field.
  • taxonkit create-taxdump:
    • fix merged.dmp and delnodes.dmp. Thanks to @apcamargo ! gtdb-taxdump/issues/2.
    • fix bug of handling non-GTDB data when using -A/--field-accession and no rank names given: the colname of the accession column would be treated as one of the ranks, which messed up all the ranks.
    • fix the default option value of --field-accession-re which wrongly remove prefix like Sp_. #65
  • taxonkit list:
    • fix warning message of merged taxids.
• TaxonKit v0.12.0
  • taxonkit create-taxdump:
    • accepts arbitrary ranks #60
    • better handle of taxa with same names.
    • many flags changed.
• TaxonKit v0.11.1
  • taxonkit create-taxdump: fix bug of missing Class rank, contributed by @apcamargo. The flag --gtdb was not effected. #57
• TaxonKit v0.11.0
  • new command taxonkit create-taxdump: Create NCBI-style taxdump files for custom taxonomy, e.g., GTDB and ICTV. #56
• TaxonKit v0.10.1
  • taxonkit cami2-filter: fix option --show-rank which did not work in v0.10.0.
• TaxonKit v0.10.0
  • new command taxonkit cami2-filter: Remove taxa of given TaxIds and their descendants in CAMI metagenomic profile
  • taxonkit reformat: fix panic for deleted taxid using -F/--fill-miss-rank. #55
• TaxonKit v0.9.0
  • new command taxonkit profile2cami: converting metagenomic profile table to CAMI format
• TaxonKit v0.8.0
  • taxonkit reformat:
    • accept input of TaxIds via flag -I/--taxid-field.
    • accept single taxonomy names.
    • show warning message for TaxIds with the same lineage. #42
    • better flag checking. #40
  • taxonkit lca:
    • slightly speedup.
  • taxonkit genautocomplete:
    • support bash|zsh|fish/powershell
• TaxonKit v0.7.2
  • taxonkit lineage:
    • new flag -R/--show-lineage-ranks for appending ranks of all levels.
    • reduce memory occupation and slightly speedup.
  • taxonkit filter:
    • flag -E/--equal-to supports multiple values.
    • new flag -n/--save-predictable-norank: do not discard some special ranks without order when using -L, where rank of the closest higher node is still lower than rank cutoff.
  • taxonkit reformat:
    • new placeholder {t} for subspecies/strain, {T} for strain. Thanks @wqssf102 for feedback.
    • new flag -S/--pseudo-strain for using the node with lowest rank as strain name, only if which rank is lower than "species" and not "subpecies" nor "strain".
• TaxonKit v0.7.1
  • taxonkit filter:
    • disable unnecessary stdin check when using flag --list-order or --list-ranks. #36
    • better handling of black list, empty default value: "no rank" and "clade". And you need use -N/--discard-noranks to explicitly filter out "no rank", "clade". #37
    • update help message. Thanks @standage for improve this command! #38
• TaxonKit v0.7.0
  • taxonkit: 2-3X faster taxonomy data loading.
  • new command taxonkit filter: filtering TaxIds by taxonomic rank range. #32
  • new command taxonkit lca: Computing lowest common ancestor (LCA) for TaxIds.
  • taxonkit reformat:
    • new flag -P/--add-prefix: add prefixes for all ranks, single prefix for a rank is defined by flag --prefix-X, where X may be k, p, c, o, f, s, S.
    • new flag -T/--trim: do not fill missing rank lower than current rank.
  • taxonkit list: do not duplicate root node.
• TaxonKit v0.6.2
  • taxonkit reformat -F: fix taxids of abbreviated lineage containing names shared by different taxids. #35
• TaxonKit v0.6.1
  • taxonkit lineage:
    • new flag -n/--show-name for appending scientific name.
    • new flag -L/--no-lineage for hide lineage, this is for fast retrieving names or/and ranks.
  • taxonkit reformat:
    • fix flag -F/--fill-miss-rank.
    • discard order restriction of rank symbols.
• TaxonKit v0.6.0
  • taxonkit list:
    • check merged and deleted taxids.
    • fix bug of json output. #30
  • taxonkit name2taxid: new flag -s/--sci-name for limiting to searching scientific names. #29
  • taxonkit version: make checking update optional
• TaxonKit v0.5.0
  • taxonkit: requiring delnodes.dmp and merged.dmp.
  • taxonkit lineage: detect deleted and merged taxids now. #19
  • taxonkit list/name2taxid: add short flag -r for --show-rank, -n for --show-name.
• TaxonKit v0.4.3
  • taxonkit taxid-changelog: rewrite logic, fix bug and add more change types
• TaxonKit v0.4.2
  • taxonkit taxid-changelog: change output of ABSORB, do not merged into one record for changes in different versions.
• TaxonKit v0.4.1
  • taxonkit taxid-changelog:
    • add fields: name and rank.
    • and fix sorting bug.
    • detailed lineage change status
• TaxonKit v0.4.0
  • new command: taxonkit taxid-changelog: for creating taxid changelog from dump archive
• TaxonKit v0.3.0
  • this version is almost the same as v0.2.5
• TaxonKit v0.2.5
  • add global flag: --line-buffered to disable output buffer. #11
  • replace global flags --names-file and --nodes-file with --data-dir, also support environment variable TAXONKIT_DB. #17
  • taxonkit reformat: detects lineages containing unofficial taxon name and won't show panic message.
  • taxonkit name2taxid: supports synonyms names. #9
  • taxokit lineage: add flag -r/--show-rank to print rank at another new column.
• TaxonKit v0.2.4
  • taxonkit reformat:
    • more accurate result when using flag -F/--fill-miss-rank to estimate and fill missing rank with original lineage information
    • supporting escape strings like \t, \n, #5
    • outputting corresponding taxids for reformated lineage. #8
  • taxonkit lineage:
    • fix bug for taxid 1 #7
    • add flag -d/--delimiter.
• TaxonKit v0.2.3
  • fix bug brought in v0.2.1
• TaxonKit v0.2.2
  • make verbose information optional #4
• TaxonKit v0.2.1
  • taxonkit list: fix bug of no output for leaf nodes of the taxonomic tree. #4
  • add new command genautocomplete to generate shell autocompletion script!
• TaxonKit v0.2.0
  • add command name2taxid to query taxid by taxon scientific name.
  • lineage, reformat: changed flags and default operations, check the usage.
• TaxonKit v0.1.8
  • taxonkit lineage, add an extra column of lineage in Taxid. #3. e.g.,
  • fix colorful output in windows.
• TaxonKit v0.1.7
  • taxonkit reformat: supports reading stdin from output of taxonkit lineage, reformated lineages are appended to input data.
• TaxonKit v0.1.6
  • remove flag -f/--formated-rank from taxonkit lineage, using taxonkit reformat can archieve same result.
• TaxonKit v0.1.5
  • reorganize code and flags
• TaxonKit v0.1.4
  • add flag --fill for taxonkit reformat, which estimates and fills missing rank with original lineage information
• TaxonKit v0.1.3
  • add command of taxonkit reformat which reformats full lineage to custom format
• TaxonKit v0.1.2
  • add command of taxonkit lineage, users can query lineage of given taxon IDs from file
• TaxonKit v0.1.1
  • add feature of taxonkit list, users can choose output in readable JSON format by flag --json so the taxonomy tree could be collapse and uncollapse in modern text editor.
• TaxonKit v0.1
  • first release