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MetaPhlAn

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution.
With StrainPhlAn, it is possible to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.


 

MetaPhlAn 4 is now available!

MetaPhlAn 4 is available in Bioconda and can be installed with Conda by running:
conda install -c bioconda metaphlan


 

MetaPhlAn 4 useful links

  • The MetaPhlAn 4 GitHub repository
  • The user manual is available here
  • For user support, please go to the BioBakery forum
  • Synthetic metagenomes containing known and unknown SGBs are available here
  • Single-isolate synthetic metagenomes at different coverages are available here

For user support, ask a question in our user support group, or contact directly the Segata lab.

MetaPhlAn 4 citation

If used MetaPhlAn 4 for your research, please consider citing the folliwing paper:

Aitor Blanco-Miguez1 Francesco Beghini1 Fabio Cumbo1 Lauren J McIver2,3 Kelsey N Thompson2,3 Moreno Zolfo1 Paolo Manghi1 Leonard Dubois1 Kun D Huang1 Andrew Maltez Thomas1 Gianmarco Piccinno1 Elisa Piperni1,4 Michal Punčochář1 Mireia Valles-Colomer1 Adrian Tett1,5 Francesca Giordano6 Richard Davies6 Jonathan Wolf6 Sarah E. Berry7 Tim D Spector8 Eric A Franzosa2,3 Edoardo Pasolli9 Francesco Asnicar1 Curtis Huttenhower2,3 Nicola Segata1,4

Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4

bioRxiv(2022) https://doi.org/10.1101/2022.08.22.504593

1 Department CIBIO, University of Trento, Italy

2 Harvard T. H. Chan School of Public Health, Boston, MA, USA

3 The Broad Institute of MIT and Harvard, Cambridge, MA, USA

4 Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy

5 Centre for Microbiology and Environmental Systems Science, University of Vienna, Austria

6 Zoe Global, London, UK

7 Department of Nutritional Sciences, King’s College London, London, UK

8 Department of Twin Research, King’s College London, London, UK

9 Department of Agricultural Sciences, University of Naples, Naples, Italy


 

MetaPhlAn 3

MetaPhlAn 3 is available in Bioconda and can be installed with Conda by running:
conda install -c bioconda metaphlan=3.1.0

Francesco Beghini1 Lauren J McIver2 Aitor Blanco-Miguez1 Leonard Dubois1 Francesco Asnicar1 Sagun Maharjan2,3 Ana Mailyan2,3 Andrew Maltez Thomas1 Paolo Manghi1 Matthias Scholz2,3 Mireia Valles-Colomer1 George Weingart2,3 Yancong Zhang2,3 Moreno Zolfo1 Curtis Huttenhower2,3 Eric A Franzosa2,3 Nicola Segata1,5

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

eLife(2021) https://doi.org/10.7554/eLife.65088

1 Department CIBIO, University of Trento, Italy

2 Harvard T. H. Chan School of Public Health, Boston, MA, USA

3 The Broad Institute of MIT and Harvard, Cambridge, MA, USA

4 Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, Italy

5 IEO, European Institute of Oncology IRCCS, Milan, Italy


 

MetaPhlAn2

If you are interested in using the previous version, MetaPhlAn2, the source code is available on GitHub.
We advise to install it using Conda by running:
conda install -c bioconda metaphlan2=2.8

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

Duy Tin Truong Eric Franzosa Timothy L Tickle Matthias Scholz George Weingart Edoardo Pasolli Adrian Tett Curtis Huttenhower Nicola Segata

Nature Methods https://doi.org/10.1038/nmeth.3589