diff --git a/README.md b/README.md index 2455584..60fb30a 100755 --- a/README.md +++ b/README.md @@ -1,69 +1,49 @@ # 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) -## An updated markers database is now available! -* Addition of ~200k new genomes -* 3,580 more SGBs than the vJan21 -* 2,548 genomes considered reference genomes in vJan21 were relabelled as MAGs in NCBI -> 1,550 kSGBs in vJan21 are now uSGBs in vOct22 -* Removed redundant reference genomes from the vJan21 genomic database using a MASH distance threshold at 0.1% -* Local reclustering to improve SGB definitions of oversized or too-close SGBs -* Improved GGB and FGB definitions by reclustering SGB centroids from scratch -* Improved phylum assignment of SGBs with no reference genomes at FGB level using MASH distances on amino acids to find the closest kSGB - -## What's new in version 4 -* Adoption of the species-level genome bins system (SGBs, http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html) -* New MetaPhlAn marker genes extracted identified from ~1M microbial genomes -* Ability to profile 21,978 known (kSGBs) and 4,992 unknown (uSGBs) microbial species -* Better representation of, not only the human gut microbiome but also many other animal and ecological environments -* Estimation of metagenome composed by microbes not included in the database with parameter `--unclassified_estimation` -* Compatibility with MetaPhlAn 3 databases with parameter `--mpa3` - -Full list of changes [here](https://github.com/biobakery/MetaPhlAn/blob/master/CHANGELOG.md). +MetaPhlAn is a computational tool for species-level microbial profiling (bacteria, archaea, eukaryotes, and viruses) from metagenomic shotgun sequencing data. +StrainPhlAn (available within MetaPhlAn) allows strain-level microbial population genomics. ------------- -## 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 StrainPhlAn, it is possible to perform accurate strain-level microbial profiling. -MetaPhlAn 4 relies on ~5.1M unique clade-specific marker genes identified from ~1M microbial genomes (~236,600 references and 771,500 metagenomic assembled genomes) spanning 26,970 species-level genome bins (SGBs, http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html), 4,992 of them taxonomically unidentified at the species level (the latest marker information file can be found [here](http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_marker_info.txt.bz2)), allowing: +### Installation -* unambiguous taxonomic assignments; -* an accurate estimation of organismal relative abundance; -* SGB-level resolution for bacteria, archaea and eukaryotes; -* strain identification and tracking -* orders of magnitude speedups compared to existing methods. -* metagenomic strain-level population genomics +To install MetaPhlan through conda run: -If you use MetaPhlAn, please cite: - -[**Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.**](https://doi.org/10.1038/s41587-023-01688-w) Aitor Blanco-Miguez, Francesco Beghini, Fabio Cumbo, Lauren J. McIver, Kelsey N. Thompson, Moreno Zolfo, Paolo Manghi, Leonard Dubois, Kun D. Huang, Andrew Maltez Thomas, Gianmarco Piccinno, Elisa Piperni, Michal Punčochář, Mireia Valles-Colomer, Adrian Tett, Francesca Giordano, Richard Davies, Jonathan Wolf, Sarah E. Berry, Tim D. Spector, Eric A. Franzosa, Edoardo Pasolli, Francesco Asnicar, Curtis Huttenhower, Nicola Segata. Nature Biotechnology (2023) - -If you use StrainPhlAn, please cite the MetaPhlAn paper and the following StrainPhlAn paper: +``` +$ conda install -c bioconda metaphlan +``` -[**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) +For further installation instructions and alternative installation methods check the [MetaPhlAn documentation](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#installation). ------------- -## 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 +### Citation +If you use MetaPhlAn, please cite: -``` -$ conda install -c bioconda metaphlan -``` +[**Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.**](https://doi.org/10.1038/s41587-023-01688-w) Aitor Blanco-Miguez, Francesco Beghini, Fabio Cumbo, Lauren J. McIver, Kelsey N. Thompson, Moreno Zolfo, Paolo Manghi, Leonard Dubois, Kun D. Huang, Andrew Maltez Thomas, Gianmarco Piccinno, Elisa Piperni, Michal Punčochář, Mireia Valles-Colomer, Adrian Tett, Francesca Giordano, Richard Davies, Jonathan Wolf, Sarah E. Berry, Tim D. Spector, Eric A. Franzosa, Edoardo Pasolli, Francesco Asnicar, Curtis Huttenhower, Nicola Segata. Nature Biotechnology (2023) -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-4#installation) paragraph. +If you use StrainPhlAn, please cite the MetaPhlAn paper and the 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 (2017) -## MetaPhlAn and StrainPhlAn tutorials and resources +If you use the MetaPhlAn viral module, please cite the MetaPhlAn paper and the MetaPhlan viral module paper: -In addition to the information on this page, you can refer to the following additional resources. +[**Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples.**](https://doi.org/10.1101/2024.02.19.580813 ) Moreno Zolfo, Andrea Silverj, Aitor Blanco-Míguez, Paolo Manghi, Omar Rota-Stabelli, Vitor Heidrich, Jordan Jensen, Sagun Maharjan, Eric Franzosa, Cristina Menni, Alessia Visconti, Federica Pinto, Matteo Ciciani, Curtis Huttenhower, Anna Cereseto, Francesco Asnicar, Hiroaki Kitano, Takuji Yamada, Nicola Segata. bioRxiv (2024) -* The [MetaPhlAn documentation](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4). +------------- -* The [StrainPhlAn documentation](https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-4). +### Tutorials and resources -* 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)). +* [MetaPhlan webpage](http://segatalab.cibio.unitn.it/tools/metaphlan/index.html) +* [MetaPhlAn documentation](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4) +* [MetaPhlan tutorial](https://github.com/biobakery/biobakery/wiki/metaphlan4) +* [MetaPhlan user support](https://forum.biobakery.org/c/microbial-community-profiling/metaphlan/) +* [MetaPhlan change log](https://github.com/biobakery/MetaPhlAn/blob/master/CHANGELOG.md) +* [StrainPhlAn webpage](http://segatalab.cibio.unitn.it/tools/strainphlan/index.html) +* [StrainPhlAn documentation](http://segatalab.cibio.unitn.it/tools/strainphlan/index.html) +* [StrainPhlan tutorial](https://github.com/biobakery/biobakery/wiki/strainphlan4) +* [StrainPhlan user support](https://forum.biobakery.org/c/microbial-community-profiling/strainphlan/) -* The related [bioBakery workflows](https://github.com/biobakery/biobakery/wiki/biobakery_workflows) +# +MetaPhlAn and StrainPhlAn are part of the bioBakery suite. For further bioBakery tools and tutorials visit the [bioBakery wiki](https://github.com/biobakery/biobakery).