MetaPhlAn: Metagenomic Phylogenetic Analysis

What's new in version 3

New MetaPhlAn marker genes extracted with a newer version of ChocoPhlAn based on UniRef
Estimation of metagenome composed by unknown microbes with parameter --unknown_estimation
Automatic retrieval and installation of the latest MetaPhlAn database with parameter --index latest
Virus profiling with --add_viruses
Calculation of metagenome size for improved estimation of reads mapped to a given clade
Inclusion of NCBI taxonomy ID in the ouput file
CAMI (Taxonomic) Profiling Output Format included
Removal of reads with low MAPQ values

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_v30_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-Miguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Andrew Maltez Thomas, Paolo Manghi, Mireia Valles-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A Franzosa, Nicola Segata. bioRxiv preprint (2020)

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)

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.

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

Metadata

Release files for metaphlan 3.0.7

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for metaphlan 3.0.7
File	Size	Uploaded
MetaPhlAn-3.0.7.tar.gz	52.8 kB	Dec 9, 2020	Details

Built distribution (wheel)

Table of built distributions (wheels) for metaphlan 3.0.7
File	Interpreter	ABI	Platform	Reset
MetaPhlAn-3.0.7-py3-none-any.whl 60.1 kB Dec 9, 2020	Python 3	none	any	Details

Total release size: 112.9 kB

Release files / MetaPhlAn-3.0.7.tar.gz

Download URL	MetaPhlAn-3.0.7.tar.gz
Size	52.8 kB
Tags	Source
SHA-256 checksum How to use checksums	`ad597ec220d549b4f6a0ae2c691ed4dc725c5034753f436ef7dcd04cf7d001e3`
BLAKE2b-256 checksum How to use checksums	`8188c5944da3038b3dfffaa29b3b84a6648b576356bc1297745d7db77025ecc6`
Upload date	Dec 9, 2020
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.2.0 pkginfo/1.6.1 requests/2.25.0 setuptools/47.1.0 requests-toolbelt/0.9.1 tqdm/4.54.1 CPython/3.7.9`

Release files / MetaPhlAn-3.0.7-py3-none-any.whl

Download URL	MetaPhlAn-3.0.7-py3-none-any.whl
Size	60.1 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`a2a65a977b7a26f3a47662d10ff545953c69b3b79b3d54f9f0ebd8453a860c8f`
BLAKE2b-256 checksum How to use checksums	`e2dc41641155623946495f68bdceed66ba0171545805ad0184b38c511f500d8e`
Upload date	Dec 9, 2020
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.2.0 pkginfo/1.6.1 requests/2.25.0 setuptools/47.1.0 requests-toolbelt/0.9.1 tqdm/4.54.1 CPython/3.7.9`