How To Install hisat2-build-l on Debian 11

One-liner install command

For those in a hurry, here's a one-line installation command:

sudo apt-get update && sudo apt -y install hisat2

But if you are interested in the detailed steps with descriptions, the following information is for you.

What is hisat2-build-l and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Debian 11. This guide was written specifically with a server running Debian 11 in mind, although it should also work on older, supported versions of the operating system.

Also, make sure you are running a regular, non-root user with sudo privileges configured on your server. When you have an account available, log in as your non-root user to begin.

There are several ways to install hisat2-build-l on Debian 11. You can use (links are clickable):

In the following sections, we will describe each method in detail. You can choose one of them or refer to the recommended one.

Install hisat2-build-l using apt-get

First, update apt database with apt-get using the following command.

sudo apt-get update

After updating apt-get database, You can install hisat2-build-l using apt by running the following command:

sudo apt -y install hisat2

Install hisat2-build-l using apt

Because hisat2-build-l is available in Debian 11’s default repositories, it is possible to install it from these repositories using the apt packaging system.

To begin, update apt database with apt using the following command.

sudo apt update

After updating apt database, You can install hisat2-build-l using apt by running the following command:

sudo apt -y install hisat2

Install hisat2-build-l 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 11. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install hisat2-build-l by running the following command:

sudo aptitude -y install hisat2

How to upgrade (update) a single package hisat2-build-l using apt-get?

First, you will need to update packages index. Run update command as usual:

sudo apt-get update

Next, to upgrade only the hisat2-build-l, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install hisat2

Note that this command will not install any new packages! If you wish to install the package if it doesn't exist you may leave out --only-upgrade part.

sudo apt-get install hisat2

How To Uninstall hisat2-build-l from Debian 11

To uninstall only the hisat2-build-l package you can execute the following command:

sudo apt-get remove hisat2

Uninstall hisat2-build-l and all its dependencies

To uninstall hisat2-build-l and its dependencies that are no longer needed by Debian 11, you can use the command below:

sudo apt-get -y autoremove hisat2

Remove hisat2-build-l with all configurations and data

To remove hisat2-build-l configuration and data from your system you can run the following purge command:

sudo apt-get -y purge hisat2

Remove hisat2-build-l completely (configurations, data and all of its dependencies)

And lastly, you can run the next command to remove absolutely everything related to hisat2-build-l package, e.g.: configurations, data and all of its dependencies. Just use this command:

sudo apt-get -y autoremove --purge hisat2

Extra info and code examples

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).

Conclusion

You now have a full guide on how to install hisat2-build-l using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the hisat2-build-l from Debian 11.

See also: