How To Install bamtools on Ubuntu 20.04

In this tutorial we learn how to install bamtools on Ubuntu 20.04. bamtools is toolkit for manipulating BAM (genome alignment) files

Introduction

In this tutorial we learn how to install bamtools on Ubuntu 20.04.

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 20.04. 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 20.04

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 20.04, 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 20.04 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 20.04 using different package management tools: apt, apt-get and aptitude.