How To Install idba on Debian 9
Introduction
In this tutorial we learn how to install idba on Debian 9.
What is idba
idba is:
IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler for transcriptome. It is purely de novo assembler based on only RNA sequencing reads. IDBA-Tran uses local assembly to reconstructing missing k-mers in low-expressed transcripts and then employs progressive cutoff on contigs to separate the graph into components. Each component corresponds to one gene in most cases and contains not many transcripts. A heuristic algorithm based on pair-end reads is then used to find the isoforms.
There are three methods to install idba on Debian 9. 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 Debian. 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 Debian 9
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 Debian 9, we can use the command below:
sudo apt-get -y autoremove idba
Remove idba Configurations and Data
To remove idba configuration and data from Debian 9 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
Dependencies
idba have the following dependencies:
References
Summary
In this tutorial we learn how to install idba package on Debian 9 using different package management tools: apt, apt-get and aptitude.