How To Install jellyfish on Ubuntu 20.04
Introduction
In this tutorial we learn how to install jellyfish
on Ubuntu 20.04.
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 Ubuntu 20.04. 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 Ubuntu. 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 Ubuntu 20.04
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 Ubuntu 20.04, we can use the command below:
sudo apt-get -y autoremove jellyfish
Remove jellyfish Configurations and Data
To remove jellyfish
configuration and data from Ubuntu 20.04 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
References
Summary
In this tutorial we learn how to install jellyfish
package on Ubuntu 20.04 using different package management tools: apt
, apt-get
and aptitude
.