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| # MetaPhlAn: Metagenomic Phylogenetic Analysis | ||
| [](http://bioconda.github.io/recipes/metaphlan/README.html) [](https://pypi.org/project/MetaPhlAn/) [](https://hub.docker.com/r/biobakery/metaphlan) [](https://github.com/biobakery/MetaPhlAn/actions?query=workflow%3A%22Build+MetaPhlAn+package%22) | ||
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| ## 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 | ||
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| ## 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` | ||
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| 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. | ||
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| ------------- | ||
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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 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 | ||
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| * 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: | ||
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| If you use MetaPhlAn, please cite: | ||
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| [**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) | ||
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| If you use StrainPhlAn, please cite the MetaPhlAn paper and the following StrainPhlAn paper: | ||
| ``` | ||
| $ conda install -c bioconda metaphlan | ||
| ``` | ||
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| [**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). | ||
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| ------------- | ||
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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](https://bioconda.github.io/user/install.html#set-up-channels) in order to setup the channels.** | ||
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| You can install MetaPhlAn by running | ||
| ### Citation | ||
| If you use MetaPhlAn, please cite: | ||
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| ``` | ||
| $ 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) | ||
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| 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: | ||
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| ------------- | ||
| [**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) | ||
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| ## MetaPhlAn and StrainPhlAn tutorials and resources | ||
| If you use the MetaPhlAn viral module, please cite the MetaPhlAn paper and the MetaPhlan viral module paper: | ||
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| 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) | ||
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| * The [MetaPhlAn documentation](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4). | ||
| ------------- | ||
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| * The [StrainPhlAn documentation](https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-4). | ||
| ### Tutorials and resources | ||
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| * 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/) | ||
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| * 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). |