How To Install pilon on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

3 minutes • 427 words

Introduction

In this tutorial we learn how to install pilon on Ubuntu.

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. 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

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, 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 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

Dependencies

pilon have the following dependencies:

References

pilon website

Summary

In this tutorial we learn how to install pilon package on Ubuntu using different package management tools: apt, apt-get and aptitude.