How To Install metaphlan on Debian 12

Learn how to install metaphlan on Debian 12 with this tutorial. metaphlan is Metagenomic Phylogenetic Analysis

Introduction

In this tutorial we learn how to install metaphlan on Debian 12.

What is metaphlan

metaphlan is:

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.

MetaPhlAn relies on ~1.1M unique clade-specific marker genes (the latest marker information file mpa_v31_CHOCOPhlAn_201901_marker_info.txt.bz2 can be found here) identified from ~100,000 reference genomes (~99,500 bacterial and archaeal and ~500 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 metaphlan on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install metaphlan Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install metaphlan using apt-get by running the following command:

sudo apt-get -y install metaphlan

Install metaphlan Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install metaphlan using apt by running the following command:

sudo apt -y install metaphlan

Install metaphlan 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 metaphlan using aptitude by running the following command:

sudo aptitude -y install metaphlan

How To Uninstall metaphlan on Debian 12

To uninstall only the metaphlan package we can use the following command:

sudo apt-get remove metaphlan

Uninstall metaphlan And Its Dependencies

To uninstall metaphlan and its dependencies that are no longer needed by Debian 12, we can use the command below:

sudo apt-get -y autoremove metaphlan

Remove metaphlan Configurations and Data

To remove metaphlan configuration and data from Debian 12 we can use the following command:

sudo apt-get -y purge metaphlan

Remove metaphlan configuration, data, and all of its dependencies

We can use the following command to remove metaphlan configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge metaphlan

Dependencies

metaphlan have the following dependencies:

References

Summary

In this tutorial we learn how to install metaphlan package on Debian 12 using different package management tools: apt, apt-get and aptitude.