How To Install jellyfish on Debian 11
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.