SAMtools is a software package for high-throughput sequencing data analysis [1]. It consists of three separate packages: SAMtools, BCFtools, and HTSlib. We are going to install SAMtools only on Ubuntu. For the installation tutorial of BCFtools, click here.

Preparing system

Open a terminal by pressing Ctrl+Alt+T. Update and upgrade your system using the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Installing Pre-requisites

To install SAMtools, you need to install some libraries that are necessary. Paste the following command in the terminal.

$ sudo apt-get install -y libncurses-dev libbz2-dev liblzma-dev

Downloading SAMtools

Change to the directory where you want to download the software. Let’s say, Downloads. Download the latest release of SAMtools from here or use the following command:

$ cd Downloads/

$ wget https://github.com/samtools/samtools/releases/download/1.12/samtools-1.12.tar.bz2

Installing SAMtools

We are in the same directory (i.e., Downloads). Now extract the downloaded package using the following commands.

$ tar xvjf samtools-1.12.tar.bz2

Now, change to the newly created directory (samtools-1.12).

$ cd samtools-1.12/

Install using the following commands.

$ ./configure

$ make

$ sudo make install

Export to the path using the following command:

$ export PATH="$PATH:/home/user/Downloads/samtools-1.12"

Now add it in the bashrc file as shown below.

• open bashrc file
  $ sudo gedit ~/.bashrc

• Add the following line at the end of the file:
  $ export PATH="$PATH:/home/user/Downloads/samtools-1.12"

• Save and exit. After that paste the following command in the terminal:
  $ source ~/.bashrc

Now, SAMtools is successfully installed on your system. You can run it by typing $ samtools.

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References

1. Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., … & Li, H. (2020). Twelve years of SAMtools and BCFtools. arXiv preprint arXiv:2012.10295.