How To Install skesa on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 411 words
Introduction
In this tutorial we learn how to install skesa on Ubuntu.
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 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 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 Ubuntu. 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 Ubuntu
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 Ubuntu, we can use the command below:
sudo apt-get -y autoremove skesa
Remove skesa Configurations and Data
To remove skesa configuration and data from Ubuntu 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 Ubuntu using different package management tools: apt, apt-get and aptitude.