Download

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

Seqkit calls pigz (much faster than gzip) or gzip to decompress .gz file if they are available. So please install pigz to gain better parsing performance for gzipped data.

Latest Version

SeqKit v0.7.1 Github Releases (by Release)

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, (mirror为中国用户下载镜像链接) Download Count
Linux 32-bit seqkit_linux_386.tar.gz, (mirror) Github Releases (by Asset)
Linux 64-bit seqkit_linux_amd64.tar.gz, (mirror) Github Releases (by Asset)
OS X 32-bit seqkit_darwin_386.tar.gz, (mirror) Github Releases (by Asset)
OS X 64-bit seqkit_darwin_amd64.tar.gz, (mirror) Github Releases (by Asset)
Windows 32-bit seqkit_windows_386.exe.tar.gz, (mirror) Github Releases (by Asset)
Windows 64-bit seqkit_windows_amd64.exe.tar.gz, (mirror) Github Releases (by Asset)

Installation

Method 1: Download binaries

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 add the current directory of the executable file to environment variable PATH:

      echo export PATH=\$PATH:\"$(pwd)\" >> ~/.bashrc
      source ~/.bashrc
      
  2. For windows, just copy seqkit.exe to C:\WINDOWS\system32.

Method 2: Install via conda Install-with-conda Anaconda Cloud downloads

conda install -c bioconda seqkit

Method 3: For Go developer

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

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