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.
