How To Install abacas on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 451 words
Introduction
In this tutorial we learn how to install abacas on Ubuntu.
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. 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
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, 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 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
Dependencies
abacas have the following dependencies:
References
Summary
In this tutorial we learn how to install abacas package on Ubuntu using different package management tools: apt, apt-get and aptitude.