MetaPhlAn

v4.1.0

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. For more information about how to use this package see README

Latest version published 3 months ago

License: MIT

PyPI

GitHub

Package Health Score

69 / 100

security
Security review needed
popularity
Small
maintenance
Healthy
community
Sustainable

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Popularity

Small

GitHub Stars: 266
Forks: 75
Contributors: 30

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package MetaPhlAn, we found that it has been starred 266 times.

Security

Security review needed

Security and license risk for latest version

Release Date: Feb 21, 2024
Direct Vulnerabilities: 0
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0
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0
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Indirect Vulnerabilities: 0
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0
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License Risk: 0
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1
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All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

MIT

Security Policy

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Maintenance

Healthy

Commit Frequency

Open Issues: 0
Open PR: 2
Last Release: 3 months ago
Last Commit: 6 days ago

Further analysis of the maintenance status of MetaPhlAn based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Healthy.

We found that MetaPhlAn demonstrates a positive version release cadence with at least one new version released in the past 3 months.

In the past month we didn't find any pull request activity or change in issues status has been detected for the GitHub repository.

Community

Sustainable

Readme: Yes
Contributing.md: No
Code of Conduct: No
Contributors: 30
Funding: No

With more than 10 contributors for the MetaPhlAn repository, this is possibly a sign for a growing and inviting community.

We found a way for you to contribute to the project! Looks like MetaPhlAn is missing a Code of Conduct.

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Package

Python Versions Compatibility: Unspecified

Age: 4 years
Latest Release: 3 months ago
Dependencies: 11 Direct / 31 Total
Versions: 25
Maintainers: 2
Wheels: OS Independent

Readme

MetaPhlAn: Metagenomic Phylogenetic Analysis

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.

Installation

To install MetaPhlan through conda run:

$ conda install -c bioconda metaphlan

For further installation instructions and alternative installation methods check the MetaPhlAn documentation.

Citation

If you use MetaPhlAn, please cite:

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. 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 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 (2017)

If you use the MetaPhlAn viral module, please cite the MetaPhlAn paper and the MetaPhlan viral module paper:

Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples. 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)

Tutorials and resources

MetaPhlAn and StrainPhlAn are part of the bioBakery suite. For further bioBakery tools and tutorials visit the bioBakery wiki.

MetaPhlAn dependencies

biom-format biopython dendropy h5py hclust2 numpy pandas phylophlan pysam requests scipy

FAQs

What is MetaPhlAn?

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryo... Visit Snyk Advisor to see a full health score report for MetaPhlAn, including popularity, security, maintenance & community analysis.

Is MetaPhlAn popular?

The python package MetaPhlAn receives a total of 1,050 weekly downloads. As such, MetaPhlAn popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is MetaPhlAn well maintained?

We found that MetaPhlAn demonstrated a healthy version release cadence and project activity. It has a community of 30 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is MetaPhlAn safe to use?

While scanning the latest version of MetaPhlAn, we found that a security review is needed. A total of 0 vulnerabilities or license issues were detected. See the full security scan results.

Last updated on 4 May-2024, at 10:00 (UTC).

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