How To Install jellyfish on Debian 11

In this tutorial we learn how to install jellyfish on Debian 11. jellyfish is count k-mers in DNA sequences

Introduction

In this tutorial we learn how to install jellyfish on Debian 11.

What is jellyfish

jellyfish is:

JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the “compare-and-swap” CPU instruction to increase parallelism.

JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the “jellyfish dump” command.

There are three methods to install jellyfish on Debian 11. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install jellyfish Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install jellyfish using apt-get by running the following command:

sudo apt-get -y install jellyfish

Install jellyfish Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install jellyfish using apt by running the following command:

sudo apt -y install jellyfish

Install jellyfish 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 jellyfish using aptitude by running the following command:

sudo aptitude -y install jellyfish

How To Uninstall jellyfish on Debian 11

To uninstall only the jellyfish package we can use the following command:

sudo apt-get remove jellyfish

Uninstall jellyfish And Its Dependencies

To uninstall jellyfish and its dependencies that are no longer needed by Debian 11, we can use the command below:

sudo apt-get -y autoremove jellyfish

Remove jellyfish Configurations and Data

To remove jellyfish configuration and data from Debian 11 we can use the following command:

sudo apt-get -y purge jellyfish

Remove jellyfish configuration, data, and all of its dependencies

We can use the following command to remove jellyfish configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge jellyfish

Dependencies

jellyfish have the following dependencies:

References

Summary

In this tutorial we learn how to install jellyfish package on Debian 11 using different package management tools: apt, apt-get and aptitude.