How To Install bowtie2 on Debian 12
Introduction
In this tutorial we learn how to install bowtie2 on Debian 12.
What is bowtie2
bowtie2 is:
is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes
There are three methods to install bowtie2 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 bowtie2 Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install bowtie2 using apt-get by running the following command:
sudo apt-get -y install bowtie2
Install bowtie2 Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install bowtie2 using apt by running the following command:
sudo apt -y install bowtie2
Install bowtie2 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 bowtie2 using aptitude by running the following command:
sudo aptitude -y install bowtie2
How To Uninstall bowtie2 on Debian 12
To uninstall only the bowtie2 package we can use the following command:
sudo apt-get remove bowtie2
Uninstall bowtie2 And Its Dependencies
To uninstall bowtie2 and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove bowtie2
Remove bowtie2 Configurations and Data
To remove bowtie2 configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge bowtie2
Remove bowtie2 configuration, data, and all of its dependencies
We can use the following command to remove bowtie2 configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge bowtie2
Dependencies
bowtie2 have the following dependencies:
References
Summary
In this tutorial we learn how to install bowtie2 package on Debian 12 using different package management tools: apt, apt-get and aptitude.