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.


OS Arch File, 中国镜像 Download Count
Linux 32-bit seqkit_linux_386.tar.gz,
Github Releases (by Asset)
Linux 64-bit seqkit_linux_amd64.tar.gz,
Github Releases (by Asset)
OS X 32-bit seqkit_darwin_386.tar.gz,
Github Releases (by Asset)
OS X 64-bit seqkit_darwin_amd64.tar.gz,
Github Releases (by Asset)
Windows 32-bit seqkit_windows_386.exe.tar.gz,
Github Releases (by Asset)
Windows 64-bit seqkit_windows_amd64.exe.tar.gz,
Github Releases (by Asset)


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

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

Install Docker

git clone this repo:

git clone

Run the following commands:

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


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


  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

Release History