How To Install ngmlr on Ubuntu 22.04
Introduction
In this tutorial we learn how to install ngmlr on Ubuntu 22.04.
What is ngmlr
ngmlr is:
Ngmlr is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith- Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments.
There are three methods to install ngmlr 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 ngmlr Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install ngmlr using apt-get by running the following command:
sudo apt-get -y install ngmlr
Install ngmlr Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install ngmlr using apt by running the following command:
sudo apt -y install ngmlr
Install ngmlr 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 ngmlr using aptitude by running the following command:
sudo aptitude -y install ngmlr
How To Uninstall ngmlr on Ubuntu 22.04
To uninstall only the ngmlr package we can use the following command:
sudo apt-get remove ngmlr
Uninstall ngmlr And Its Dependencies
To uninstall ngmlr and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove ngmlr
Remove ngmlr Configurations and Data
To remove ngmlr configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge ngmlr
Remove ngmlr configuration, data, and all of its dependencies
We can use the following command to remove ngmlr configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge ngmlr
References
Summary
In this tutorial we learn how to install ngmlr package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
