How To Install bamtools on Ubuntu 22.04
Introduction
In this tutorial we learn how to install bamtools
on Ubuntu 22.04.
What is bamtools
bamtools is:
BamTools facilitates research analysis and data management using BAM files. It copes with the enormous amount of data produced by current sequencing technologies that is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research.
BamTools provides both a C++ API for BAM file support as well as a command-line toolkit.
This is the bamtools command-line toolkit.
Available bamtools commands: convert Converts between BAM and a number of other formats count Prints number of alignments in BAM file(s) coverage Prints coverage statistics from the input BAM file filter Filters BAM file(s) by user-specified criteria header Prints BAM header information index Generates index for BAM file merge Merge multiple BAM files into single file random Select random alignments from existing BAM file(s), intended more as a testing tool. resolve Resolves paired-end reads (marking the IsProperPair flag as needed) revert Removes duplicate marks and restores original base qualities sort Sorts the BAM file according to some criteria split Splits a BAM file on user-specified property, creating a new BAM output file for each value found stats Prints some basic statistics from input BAM file(s)
There are three methods to install bamtools
on Ubuntu 22.04. We can use apt-get
, apt
and aptitude
. In the following sections we will describe each method. You can choose one of them.
Install bamtools Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install bamtools
using apt-get
by running the following command:
sudo apt-get -y install bamtools
Install bamtools Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install bamtools
using apt
by running the following command:
sudo apt -y install bamtools
Install bamtools 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 bamtools
using aptitude
by running the following command:
sudo aptitude -y install bamtools
How To Uninstall bamtools on Ubuntu 22.04
To uninstall only the bamtools
package we can use the following command:
sudo apt-get remove bamtools
Uninstall bamtools And Its Dependencies
To uninstall bamtools
and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove bamtools
Remove bamtools Configurations and Data
To remove bamtools
configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge bamtools
Remove bamtools configuration, data, and all of its dependencies
We can use the following command to remove bamtools
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge bamtools
References
Summary
In this tutorial we learn how to install bamtools
package on Ubuntu 22.04 using different package management tools: apt
, apt-get
and aptitude
.