Metadata-Version: 2.1
Name: MetaPhlAn
Version: 3.0.7
Summary: 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.
Home-page: http://github.com/biobakery/MetaPhlAn/
Author: Francesco Beghini
Author-email: francesco.beghini@unitn.it
License: LICENSE.txt
Description: # MetaPhlAn: Metagenomic Phylogenetic Analysis
        [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/metaphlan/README.html) [![PyPI - Downloads](https://img.shields.io/pypi/dm/metaphlan?label=MetaPhlAn%20on%20PyPi)](https://pypi.org/project/MetaPhlAn/) [![MetaPhlAn on DockerHub](https://img.shields.io/docker/pulls/biobakery/metaphlan?label=MetaPhlAn%20on%20DockerHub)](https://hub.docker.com/r/biobakery/metaphlan) [![Build MetaPhlAn package](https://github.com/biobakery/MetaPhlAn/workflows/Build%20MetaPhlAn%20package/badge.svg?branch=3.0)](https://github.com/biobakery/MetaPhlAn/actions?query=workflow%3A%22Build+MetaPhlAn+package%22)
        ## 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](https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AAAlyQITZuUCtBUJxpxhIroIa/mpa_v30_CHOCOPhlAn_201901_marker_info.txt.bz2?dl=1)) 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**](https://www.biorxiv.org/content/10.1101/2020.11.19.388223v1) *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.**](http://genome.cshlp.org/content/27/4/626.full.pdf) *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](https://bioconda.github.io/user/install.html#set-up-channels) 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](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-3.0#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](https://github.com/biobakery/MetaPhlAn/wiki).
        
        * The [StrainPhlAn tutorial](https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-3.0).
        
        * The [MetaPhlAn](https://github.com/biobakery/biobakery/wiki/metaphlan3) and [StrainPhlAn](https://github.com/biobakery/biobakery/wiki/strainphlan3) wikis on bioBakery.
        
        * The [MetaPhlAn](https://forum.biobakery.org/c/Microbial-community-profiling/MetaPhlAn/) and [StrainPhlAn](https://forum.biobakery.org/c/Microbial-community-profiling/StrainPhlAn/) Discourse forum.
        
        * Related tools including [PanPhlAn](https://github.com/segatalab/panphlan) (and its [tutorial](https://github.com/segatalab/panphlan/wiki/Home)), [GraPhlAn](https://github.com/segatalab/graphlan) (and it [tutorial](https://github.com/biobakery/biobakery/wiki/graphlan)), [PhyloPhlAn 3](https://github.com/biobakery/phylophlan) (and its [tutorial](https://github.com/biobakery/biobakery/wiki/phylophlan)), [HUMAnN](https://github.com/biobakery/humann/) (and its [tutorial](https://github.com/biobakery/biobakery/wiki/humann2)).
        
        * The related [bioBakery workflows](https://github.com/biobakery/biobakery/wiki/biobakery_workflows)
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