How To Install pilon on Ubuntu 22.04
Introduction
In this tutorial we learn how to install pilon on Ubuntu 22.04.
What is pilon
pilon is:
Pilon is a software tool which can be used to:
- Automatically improve draft assemblies
- Find variation among strains, including large event detection Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:
- Single base differences
- Small indels
- Larger indel or block substitution events
- Gap filling
- Identification of local misassemblies, including optional opening of new gaps
There are three methods to install pilon 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 pilon Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install pilon using apt-get by running the following command:
sudo apt-get -y install pilon
Install pilon Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install pilon using apt by running the following command:
sudo apt -y install pilon
Install pilon 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 pilon using aptitude by running the following command:
sudo aptitude -y install pilon
How To Uninstall pilon on Ubuntu 22.04
To uninstall only the pilon package we can use the following command:
sudo apt-get remove pilon
Uninstall pilon And Its Dependencies
To uninstall pilon and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove pilon
Remove pilon Configurations and Data
To remove pilon configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge pilon
Remove pilon configuration, data, and all of its dependencies
We can use the following command to remove pilon configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge pilon
References
Summary
In this tutorial we learn how to install pilon package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
