How To Install samtools on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 400 words
Introduction
In this tutorial we learn how to install samtools on Ubuntu.
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 Ubuntu. 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 first since aptitude is usually not installed by default on Ubuntu. 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 Ubuntu
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 Ubuntu, we can use the command below:
sudo apt-get -y autoremove samtools
Remove samtools Configurations and Data
To remove samtools configuration and data from Ubuntu 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:
References
Summary
In this tutorial we learn how to install samtools package on Ubuntu using different package management tools: apt, apt-get and aptitude.