Introduction
In this tutorial we learn how to install centrifuge
on Ubuntu 20.04.
What is centrifuge
centrifuge is:
Centrifuge is a very rapid and memory-efficient system for the
classification of DNA sequences from microbial samples, with better
sensitivity than and comparable accuracy to other leading systems. The
system uses a novel indexing scheme based on the Burrows-Wheeler
transform (BWT) and the Ferragina-Manzini (FM) index, optimized
specifically for the metagenomic classification problem. Centrifuge
requires a relatively small index (e.g., 4.3 GB for ~4,100 bacterial
genomes) yet provides very fast classification speed, allowing it to
process a typical DNA sequencing run within an hour. Together these
advances enable timely and accurate analysis of large metagenomics data
sets on conventional desktop computers.
There are three methods to install centrifuge
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 centrifuge Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install centrifuge
using apt-get
by running the following command:
sudo apt-get -y install centrifuge
Install centrifuge Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install centrifuge
using apt
by running the following command:
sudo apt -y install centrifuge
Install centrifuge 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 centrifuge
using aptitude
by running the following command:
sudo aptitude -y install centrifuge
How To Uninstall centrifuge on Ubuntu 20.04
To uninstall only the centrifuge
package we can use the following command:
sudo apt-get remove centrifuge
Uninstall centrifuge And Its Dependencies
To uninstall centrifuge
and its dependencies that are no longer needed by Ubuntu 20.04, we can use the command below:
sudo apt-get -y autoremove centrifuge
Remove centrifuge Configurations and Data
To remove centrifuge
configuration and data from Ubuntu 20.04 we can use the following command:
sudo apt-get -y purge centrifuge
Remove centrifuge configuration, data, and all of its dependencies
We can use the following command to remove centrifuge
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge centrifuge
References
Summary
In this tutorial we learn how to install centrifuge
package on Ubuntu 20.04 using different package management tools: apt
, apt-get
and aptitude
.