How To Install samtools on Kali Linux

Introduction

In this tutorial we learn how to install samtools on Kali Linux.

What is samtools

samtools is:

Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM (Sequence Alignment/Map) and CRAM formats, does sorting, merging and indexing, and allows one to retrieve reads in any regions swiftly. It is designed to work on a stream, and is able to open a BAM or CRAM (not SAM) file on a remote FTP or HTTP server.

There are three methods to install samtools on Kali Linux. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install samtools Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install samtools using apt-get by running the following command:

sudo apt-get -y install samtools

Install samtools Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install samtools using apt by running the following command:

sudo apt -y install samtools

Install samtools Using aptitude

If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install samtools using aptitude by running the following command:

sudo aptitude -y install samtools

How To Uninstall samtools on Kali Linux

To uninstall only the samtools package we can use the following command:

sudo apt-get remove samtools

Uninstall samtools And Its Dependencies

To uninstall samtools and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove samtools

Remove samtools Configurations and Data

To remove samtools configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge samtools

Remove samtools configuration, data, and all of its dependencies

We can use the following command to remove samtools configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge samtools

Dependencies

samtools have the following dependencies:

• libc6
• libhts3
• libncurses6
• libtinfo6
• zlib1g

References

• samtools website

Summary

In this tutorial we learn how to install samtools package on Kali Linux using different package management tools: apt, apt-get and aptitude.