How To Install idba-extra on Kali Linux
Introduction
In this tutorial we learn how to install idba-extra on Kali Linux.
What is idba-extra
idba-extra is:
IDBA stands for iterative de Bruijn graph assembler. In computational sequence biology, an assembler solves the puzzle coming from large sequencing machines that feature many gigabytes of short reads from a large genome.
This package provides several flavours of the IDBA assembler, as they all share the same source tree but serve different purposes and evolved over time.
IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a generic purpose assembler and especially good for single-cell and metagenomic sequencing data. IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for RNA-Seq data.
This package ships extra tools for using idba in specific situations.
There are three methods to install idba-extra 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 idba-extra Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install idba-extra using apt-get by running the following command:
sudo apt-get -y install idba-extraInstall idba-extra Using apt
Update apt database with apt using the following command.
sudo apt updateAfter updating apt database, We can install idba-extra using apt by running the following command:
sudo apt -y install idba-extraInstall idba-extra Using aptitude
If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.
sudo aptitude updateAfter updating apt database, We can install idba-extra using aptitude by running the following command:
sudo aptitude -y install idba-extraHow To Uninstall idba-extra on Kali Linux
To uninstall only the idba-extra package we can use the following command:
sudo apt-get remove idba-extraUninstall idba-extra And Its Dependencies
To uninstall idba-extra and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove idba-extraRemove idba-extra Configurations and Data
To remove idba-extra configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge idba-extraRemove idba-extra configuration, data, and all of its dependencies
We can use the following command to remove idba-extra configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge idba-extraDependencies
idba-extra have the following dependencies:
References
Summary
In this tutorial we learn how to install idba-extra package on Kali Linux using different package management tools: apt, apt-get and aptitude.