How to Install and Uninstall hisat2 Ubuntu 22.04

Updated: September 3, 2022

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). I will show you how to install hisat2 on Ubuntu 22.04 in this guide.

Prerequisites

  • Operating system: hisat2 needs Ubuntu 22.04 to work
  • Privileges: Make sure that you can run the sudo commands line.

Prerequisites to install hisat2 on Ubuntu 22.04

Install hisat2 Ubuntu 22.04

hisat2 is one of the popular ways on Ubuntu now so that this tutorial will show you how to install it in various ways. Choose the one you believe is simple and easy to follow.

Install hisat2 using APT

This is a popular method for installing any Ubuntu packages because it’s easy to follow, even if you are a newbie in Linux. Following these steps to install hisat2 on your Ubuntu.

Step 1: The APT package repository cache needs to be updated before you try to install, update, or remove any packages. Update the APT database to download new packages from Ubuntu. Launching the terminal and entering the following Linux command:

sudo apt-get -y update

Step 2: Start the package installation on Ubuntu 22.04. After updating, you can install hisat2 Ubuntu by executing this command in the terminal.

sudo apt install hisat2

Install hisat2 using Aptitude

Aptitude allows users to view a list of available packages and manage package installation, upgrade, and removal. If you haven’t already done so, run this command to install it.

sudo apt install aptitude

After that, you can now install hisat2 by following these steps:

Step 1: You must update the APT package repository cache before attempting to install, update, or remove any packages. Update the APT database to download new packages from Ubuntu. Launch the terminal and enter the following Linux command:

sudo apt-get update

Step 2: Start the package installation on Ubuntu 22.04. After updating the system, you can install hisat2 Ubuntu by executing this command in the terminal.

sudo aptitude -y install hisat2

Uninstall hisat2 on Ubuntu 22.04

Have you ever considered how difficult it is to uninstall an application from Ubuntu? You are mistaken; anyone, not just package administrators, can easily uninstall any program.

You can uninstall hisat2 Ubuntu by running this command if you installed it using APT or Aptitude.

sudo apt remove --auto-remove hisat2

To uninstall hisat2 and remove its data and dependencies, you can also use the following command:

sudo apt autoremove --purge hisat2

Conclusion

In this guide, I showed you ways to install hisat2 on Ubuntu 22.04 and some ways to uninstall hisat2 too. Please do not hesitate to contact me if you require assistance. I’m delighted to respond.