pkonieczny / metaphlan

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

MetaPhlAn: Metagenomic Phylogenetic Analysis

What's new in version 3.1

• 433 low-quality species were removed from the MetaPhlAn 3.1 marker database and 2,680 species were added (for a new total of 15,766; a 17% increase).
• Marker genes for a subset of existing bioBakery 3 species were also revised.
• Most existing bioBakery 3 species pangenomes were updated with revised or expanded gene content.
• MetaPhlAn 3.1 software has been updated to work with revised marker database.

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Description

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

If you use MetaPhlAn, please cite:

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 Francesco Beghini, Lauren J McIver, Aitor Blanco-Míguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Paolo Manghi, Matthias Scholz, Andrew Maltez Thomas, Mireia Valles-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A Franzosa, Nicola Segata. eLife (2021)

If you use StrainPhlAn, please cite the MetaPhlAn paper and the following StrainPhlAn paper:

Microbial strain-level population structure and genetic diversity from metagenomes. Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis Huttenhower, & Nicola Segata. Genome Research 27:626-638 (2017)

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Installation

The best way to install MetaPhlAn is through conda via the Bioconda channel. If you have not configured you Anaconda installation in order to fetch packages from Bioconda, please follow these steps in order to setup the channels.

You can install MetaPhlAn by running

$ conda install -c bioconda python=3.7 metaphlan

For installing it from the source code and for further installation instructions, please see the Wiki at the Installation paragraph.

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MetaPhlAn and StrainPhlAn tutorials and resources

In addition to the information on this page, you can refer to the following additional resources.

• The MetaPhlAn tutorial.

• The StrainPhlAn tutorial.

• The MetaPhlAn and StrainPhlAn wikis on bioBakery.

• The MetaPhlAn and StrainPhlAn Discourse forum.

• Related tools including PanPhlAn (and its tutorial), GraPhlAn (and it tutorial), PhyloPhlAn 3 (and its tutorial), HUMAnN (and its tutorial).

• The related bioBakery workflows