How To Install abacas on Kali Linux

In this tutorial we learn how to install abacas on Kali Linux. abacas is close gaps in genomic alignments from short reads

Introduction

In this tutorial we learn how to install abacas on Kali Linux.

What is abacas

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 ways to install abacas on Kali Linux . 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 Kali Linux. 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 Kali Linux

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 Kali Linux, we can use the command below:

sudo apt-get -y autoremove abacas

Remove abacas Configurations and Data

To remove abacas configuration and data from Kali Linux 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 using different package management tools like apt, apt-get and aptitude.