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

Latest Version

Please cite

W Shen, S Le, Y Li*, F Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS ONE. doi:10.1371/journal.pone.0163962.

Tips

OS Arch File, 中国镜像 Download Count
Linux 32-bit seqkit_linux_386.tar.gz,
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Linux 64-bit seqkit_linux_amd64.tar.gz,
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OS X 32-bit seqkit_darwin_386.tar.gz,
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OS X 64-bit seqkit_darwin_amd64.tar.gz,
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Windows 32-bit seqkit_windows_386.exe.tar.gz,
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Windows 64-bit seqkit_windows_amd64.exe.tar.gz,
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Installation

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 seqkit /usr/local/bin/
      
    2. Or copy to anywhere in the environment variable PATH:

      mkdir -p $HOME/bin/; cp seqkit $HOME/bin/
      
  2. For windows, just copy seqkit.exe to C:\WINDOWS\system32.

Method 2: Install via conda (latest stable version) Install-with-conda Anaconda Cloud downloads

conda install -c bioconda seqkit

Method 3: Install via homebrew (latest stable version)

brew install brewsci/bio/seqkit

Method 4: For Go developer (latest stable/dev version)

go get -u github.com/shenwei356/seqkit/seqkit

Method 5: Docker based installation (latest stable/dev version)

Install Docker

git clone this repo:

git clone https://github.com/shenwei356/seqkit

Run the following commands:

cd seqkit
docker build -t shenwei356/seqkit .
docker run -it shenwei356/seqkit:latest

Bash-completion

Note: The current version supports Bash only. This should work for *nix systems with Bash installed.

Howto:

  1. run: seqkit 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
    

Release History