How To Install hisat2 on Ubuntu 22.04
Introduction
In this tutorial we learn how to install hisat2 on Ubuntu 22.04.
What is hisat2
hisat2 is:
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome). Based on an extension of BWT for graphs a graph FM index (GFM) was designed and implementd. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).
There are three methods to install hisat2 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 hisat2 Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install hisat2 using apt-get by running the following command:
sudo apt-get -y install hisat2
Install hisat2 Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install hisat2 using apt by running the following command:
sudo apt -y install hisat2
Install hisat2 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 hisat2 using aptitude by running the following command:
sudo aptitude -y install hisat2
How To Uninstall hisat2 on Ubuntu 22.04
To uninstall only the hisat2 package we can use the following command:
sudo apt-get remove hisat2
Uninstall hisat2 And Its Dependencies
To uninstall hisat2 and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove hisat2
Remove hisat2 Configurations and Data
To remove hisat2 configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge hisat2
Remove hisat2 configuration, data, and all of its dependencies
We can use the following command to remove hisat2 configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge hisat2
References
Summary
In this tutorial we learn how to install hisat2 package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
