How To Install metaphlan2 on Ubuntu 22.04
Introduction
In this tutorial we learn how to install metaphlan2 on Ubuntu 22.04.
What is metaphlan2
metaphlan2 is:
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. From version 2.0, MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.
MetaPhlAn 2.0 relies on ~1M unique clade-specific marker genes (the marker information file can be found at usr/share/metaphlan2/utils/markers_info.txt.bz2) identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic), allowing:
- unambiguous taxonomic assignments;
- accurate estimation of organismal relative abundance;
- species-level resolution for bacteria, archaea, eukaryotes and viruses;
- strain identification and tracking
- orders of magnitude speedups compared to existing methods.
- metagenomic strain-level population genomics
There are three methods to install metaphlan2 on Ubuntu 22.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install metaphlan2 Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install metaphlan2 using apt-get by running the following command:
sudo apt-get -y install metaphlan2
Install metaphlan2 Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install metaphlan2 using apt by running the following command:
sudo apt -y install metaphlan2
Install metaphlan2 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 metaphlan2 using aptitude by running the following command:
sudo aptitude -y install metaphlan2
How To Uninstall metaphlan2 on Ubuntu 22.04
To uninstall only the metaphlan2 package we can use the following command:
sudo apt-get remove metaphlan2
Uninstall metaphlan2 And Its Dependencies
To uninstall metaphlan2 and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove metaphlan2
Remove metaphlan2 Configurations and Data
To remove metaphlan2 configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge metaphlan2
Remove metaphlan2 configuration, data, and all of its dependencies
We can use the following command to remove metaphlan2 configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge metaphlan2
References
Summary
In this tutorial we learn how to install metaphlan2 package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
