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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 VersionLink

  • TaxonKit v0.16.0 Github Releases (by Release)
    • taxonkit create-taxdump:
      • TaxIds are generated from the hash value of "rank+taxon_name", this allowed duplicated names with different ranks (common in GTDB). #92.
    • taxonkit taxid-changelog/create-taxdump:
      • Add notes about the possible error records in taxid-changelog built from taxonomic data created by create-taxdump. #91
      • Dont't worry, a single version of taxonomic data created by taxonkit create-taxdump has no problem, it's just the changelog might not be perfect.
    • taxonkit lca:
      • new flag -K/--keep-invalid: print the query even if no single valid taxid left. #89

Please citeLink

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

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
Github Releases (by Asset)
Linux arm64 taxonkit_linux_arm64.tar.gz,
中国镜像
Github Releases (by Asset)
macOS 64-bit taxonkit_darwin_amd64.tar.gz,
中国镜像
Github Releases (by Asset)
macOS arm64 taxonkit_darwin_arm64.tar.gz,
中国镜像
Github Releases (by Asset)
Windows 64-bit taxonkit_windows_amd64.exe.tar.gz,
中国镜像
Github Releases (by Asset)

InstallationLink

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)Link

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) Install-with-conda Anaconda Cloud downloadsLink

conda install -c bioconda taxonkit

Method 3: Install via homebrew (may not the lastest version)Link

brew install brewsci/bio/taxonkit

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

  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-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

DatasetLink

  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 historyLink

  • TaxonKit v0.15.1 Github Releases (by Release)
    • taxonkit name2taxid:
      • remove the restriction of name types. #87
  • TaxonKit v0.15.0 Github Releases (by Release)
    • taxonkit reformat:
      • For lineages with more than one node, if it fails to query TaxId with the parent-child pair, use the last child only. #82
      • The flag -T/--trim also does not add the prefix for missing ranks lower than the current rank. #82
      • New flag -s/--miss-rank-repl-suffix to set the suffix for estimated taxon names. #85
  • TaxonKit v0.14.2 Github Releases (by Release)
    • 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
  • TaxonKit v0.14.1 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • taxonkit create-taxdump:
      • accepts arbitrary ranks #60
      • better handle of taxa with same names.
      • many flags changed.
  • TaxonKit v0.11.1 Github Releases (by Release)
    • taxonkit create-taxdump: fix bug of missing Class rank, contributed by @apcamargo. The flag --gtdb was not effected. #57
  • TaxonKit v0.11.0 Github Releases (by Release)
    • new command taxonkit create-taxdump: Create NCBI-style taxdump files for custom taxonomy, e.g., GTDB and ICTV. #56
  • TaxonKit v0.10.1 Github Releases (by Release)
    • taxonkit cami2-filter: fix option --show-rank which did not work in v0.10.0.
  • TaxonKit v0.10.0 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • new command taxonkit profile2cami: converting metagenomic profile table to CAMI format
  • TaxonKit v0.8.0 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • taxonkit reformat -F: fix taxids of abbreviated lineage containing names shared by different taxids. #35
  • TaxonKit v0.6.1 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • taxonkit taxid-changelog: rewrite logic, fix bug and add more change types
  • TaxonKit v0.4.2 Github Releases (by Release)
    • taxonkit taxid-changelog: change output of ABSORB, do not merged into one record for changes in different versions.
  • TaxonKit v0.4.1 Github Releases (by Release)
    • taxonkit taxid-changelog:
      • add fields: name and rank.
      • and fix sorting bug.
      • detailed lineage change status
  • TaxonKit v0.4.0 Github Releases (by Release)
    • new command: taxonkit taxid-changelog: for creating taxid changelog from dump archive
  • TaxonKit v0.3.0 Github Releases (by Release)
    • this version is almost the same as v0.2.5
  • TaxonKit v0.2.5 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • fix bug brought in v0.2.1
  • TaxonKit v0.2.2 Github Releases (by Release)
    • make verbose information optional #4
  • TaxonKit v0.2.1 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • add command name2taxid to query taxid by taxon scientific name.
    • lineage, reformat: changed flags and default operations, check the usage.
  • TaxonKit v0.1.8 Github Releases (by Release)
    • taxonkit lineage, add an extra column of lineage in Taxid. #3. e.g.,
    • fix colorful output in windows.
  • TaxonKit v0.1.7 Github Releases (by Release)
    • taxonkit reformat: supports reading stdin from output of taxonkit lineage, reformated lineages are appended to input data.
  • TaxonKit v0.1.6 Github Releases (by Release)
    • remove flag -f/--formated-rank from taxonkit lineage, using taxonkit reformat can archieve same result.
  • TaxonKit v0.1.5 Github Releases (by Release)
    • reorganize code and flags
  • TaxonKit v0.1.4 Github Releases (by Release)
    • add flag --fill for taxonkit reformat, which estimates and fills missing rank with original lineage information
  • TaxonKit v0.1.3 Github Releases (by Release)
    • add command of taxonkit reformat which reformats full lineage to custom format
  • TaxonKit v0.1.2 Github Releases (by Release)
    • add command of taxonkit lineage, users can query lineage of given taxon IDs from file
  • TaxonKit v0.1.1 Github Releases (by Release)
    • 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 Github Releases (by Release)
    • first release