How To Install skesa on Debian 12

Learn how to install skesa on Debian 12 with this tutorial. skesa is strategic Kmer extension for scrupulous assemblies

Introduction

In this tutorial we learn how to install skesa on Debian 12.

What is `skesa`

skesa is:

SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity, handles low-level contamination in reads, is fast, and produces an identical assembly for the same input when assembled multiple times with the same or different compute resources. SKESA has been used for assembling over 272,000 read sets in the Sequence Read Archive at NCBI and for real-time pathogen detection.

There are three methods to install skesa on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install skesa Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install skesa using apt-get by running the following command:

sudo apt-get -y install skesa

Install skesa Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install skesa using apt by running the following command:

sudo apt -y install skesa

Install skesa 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 skesa using aptitude by running the following command:

sudo aptitude -y install skesa

How To Uninstall skesa on Debian 12

To uninstall only the skesa package we can use the following command:

sudo apt-get remove skesa

Uninstall skesa And Its Dependencies

To uninstall skesa and its dependencies that are no longer needed by Debian 12, we can use the command below:

sudo apt-get -y autoremove skesa

Remove skesa Configurations and Data

To remove skesa configuration and data from Debian 12 we can use the following command:

sudo apt-get -y purge skesa

Remove skesa configuration, data, and all of its dependencies

We can use the following command to remove skesa configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge skesa

Dependencies

skesa have the following dependencies:

References

Summary

In this tutorial we learn how to install skesa package on Debian 12 using different package management tools: apt, apt-get and aptitude.