How To Install idba on Ubuntu 22.04

In this tutorial we learn how to install idba on Ubuntu 22.04. idba is iterative De Bruijn Graph short read assemblers

Introduction

In this tutorial we learn how to install idba on Ubuntu 22.04.

What is idba

idba 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.

There are three methods to install idba on Ubuntu 22.04. 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 Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install idba

Install idba Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install idba

Install idba 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 idba using aptitude by running the following command:

sudo aptitude -y install idba

How To Uninstall idba on Ubuntu 22.04

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

sudo apt-get remove idba

Uninstall idba And Its Dependencies

To uninstall idba and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:

sudo apt-get -y autoremove idba

Remove idba Configurations and Data

To remove idba configuration and data from Ubuntu 22.04 we can use the following command:

sudo apt-get -y purge idba

Remove idba configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge idba

References

Summary

In this tutorial we learn how to install idba package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.