How To Install jellyfish1 on Debian 10
Introduction
In this tutorial we learn how to install jellyfish1 on Debian 10.
What is jellyfish1
jellyfish1 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.
This is the latest version of the 1.x series of jellyfish which is used by some other applications that are not compatible with version 2.x which is provided inside the jellyfish package.
There are three methods to install jellyfish1 on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install jellyfish1 Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install jellyfish1 using apt-get by running the following command:
sudo apt-get -y install jellyfish1
Install jellyfish1 Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install jellyfish1 using apt by running the following command:
sudo apt -y install jellyfish1
Install jellyfish1 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 jellyfish1 using aptitude by running the following command:
sudo aptitude -y install jellyfish1
How To Uninstall jellyfish1 on Debian 10
To uninstall only the jellyfish1 package we can use the following command:
sudo apt-get remove jellyfish1
Uninstall jellyfish1 And Its Dependencies
To uninstall jellyfish1 and its dependencies that are no longer needed by Debian 10, we can use the command below:
sudo apt-get -y autoremove jellyfish1
Remove jellyfish1 Configurations and Data
To remove jellyfish1 configuration and data from Debian 10 we can use the following command:
sudo apt-get -y purge jellyfish1
Remove jellyfish1 configuration, data, and all of its dependencies
We can use the following command to remove jellyfish1 configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge jellyfish1
Dependencies
jellyfish1 have the following dependencies:
References
Summary
In this tutorial we learn how to install jellyfish1 package on Debian 10 using different package management tools: apt, apt-get and aptitude.
