How To Install ragout on Debian 11
Introduction
In this tutorial we learn how to install ragout on Debian 11.
What is ragout
ragout is:
Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome-level scaffolding using multiple references. Given initial assembly fragments (contigs/scaffolds) and one or multiple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds).
The approach is based on the analysis of genome rearrangements (like inversions or chromosomal translocations) between the input genomes and reconstructing the most parsimonious structure of the target genome.
Ragout now supports both small and large genomes (of mammalian scale and complexity). The assembly of highly polymorphic genomes is currently limited.
There are three methods to install ragout on Debian 11. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install ragout Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install ragout using apt-get by running the following command:
sudo apt-get -y install ragout
Install ragout Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install ragout using apt by running the following command:
sudo apt -y install ragout
Install ragout 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 Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install ragout using aptitude by running the following command:
sudo aptitude -y install ragout
How To Uninstall ragout on Debian 11
To uninstall only the ragout package we can use the following command:
sudo apt-get remove ragout
Uninstall ragout And Its Dependencies
To uninstall ragout and its dependencies that are no longer needed by Debian 11, we can use the command below:
sudo apt-get -y autoremove ragout
Remove ragout Configurations and Data
To remove ragout configuration and data from Debian 11 we can use the following command:
sudo apt-get -y purge ragout
Remove ragout configuration, data, and all of its dependencies
We can use the following command to remove ragout configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge ragout
Dependencies
ragout have the following dependencies:
References
Summary
In this tutorial we learn how to install ragout package on Debian 11 using different package management tools: apt, apt-get and aptitude.