Introduction
In this tutorial we learn how to install abacas on Ubuntu 22.04.
What is abacas
abacas is:
ABACAS (Algorithm Based Automatic Contiguation of Assembled Sequences)
intends to rapidly contiguate (align, order, orientate), visualize and
design primers to close gaps on shotgun assembled contigs based on a
reference sequence.
ABACAS uses MUMmer to find alignment positions and identify syntenies
of assembled contigs against the reference. The output is then processed
to generate a pseudomolecule taking overlapping contigs and gaps in to
account. ABACAS generates a comparison file that can be used to
visualize ordered and oriented contigs in ACT. Synteny is represented by
red bars where colour intensity decreases with lower values of percent
identity between comparable blocks. Information on contigs such as the
orientation, percent identity, coverage and overlap with other contigs
can also be visualized by loading the outputted feature file on ACT.
There are three methods to install abacas 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 abacas Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install abacas using apt-get by running the following command:
sudo apt-get -y install abacas
Install abacas Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install abacas using apt by running the following command:
sudo apt -y install abacas
Install abacas 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 abacas using aptitude by running the following command:
sudo aptitude -y install abacas
How To Uninstall abacas on Ubuntu 22.04
To uninstall only the abacas package we can use the following command:
sudo apt-get remove abacas
Uninstall abacas And Its Dependencies
To uninstall abacas and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove abacas
Remove abacas Configurations and Data
To remove abacas configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge abacas
Remove abacas configuration, data, and all of its dependencies
We can use the following command to remove abacas configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge abacas
References
Summary
In this tutorial we learn how to install abacas package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
