metaphlan
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Science Score: 39.0%
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○CITATION.cff file
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✓codemeta.json file
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✓DOI references
Found 4 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (9.5%) to scientific vocabulary
Keywords
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Repository
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Basic Info
- Host: GitHub
- Owner: biobakery
- License: mit
- Language: Python
- Default Branch: master
- Homepage: http://segatalab.cibio.unitn.it/tools/metaphlan/index.html
- Size: 7.57 MB
Statistics
- Stars: 363
- Watchers: 20
- Forks: 92
- Open Issues: 4
- Releases: 28
Topics
Metadata Files
README.md
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 webpage
- MetaPhlAn documentation
- MetaPhlan tutorial
- MetaPhlan user support
- MetaPhlan change log
- StrainPhlAn webpage
- StrainPhlAn documentation
- StrainPhlan tutorial
- StrainPhlan user support
MetaPhlAn and StrainPhlAn are part of the bioBakery suite. For further bioBakery tools and tutorials visit the bioBakery wiki.
Owner
- Name: bioBakery
- Login: biobakery
- Kind: organization
- Website: http://huttenhower.sph.harvard.edu/
- Repositories: 24
- Profile: https://github.com/biobakery
Software, documentation, and tutorials for microbial community profiling.
GitHub Events
Total
- Create event: 7
- Release event: 5
- Issues event: 8
- Watch event: 53
- Delete event: 3
- Issue comment event: 6
- Push event: 62
- Gollum event: 2
- Pull request event: 3
- Fork event: 4
Last Year
- Create event: 7
- Release event: 5
- Issues event: 8
- Watch event: 53
- Delete event: 3
- Issue comment event: 6
- Push event: 62
- Gollum event: 2
- Pull request event: 3
- Fork event: 4
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Francesco Beghini | f****i@u****t | 221 |
| duytin | 1****g | 131 |
| Aitor Blanco | b****z@g****m | 92 |
| Nicola Segata | n****a@u****t | 86 |
| Francesco Asnicar | f****r@u****t | 83 |
| Francesco Beghini | f****i@o****m | 45 |
| Claudia Mengoni | 4****i | 25 |
| Michal Puncochar | m****r@g****m | 23 |
| ljmciver | l****r@g****m | 21 |
| Afrah Shafquat | a****t@g****m | 12 |
| Moreno | m****o@g****m | 8 |
| Vitor Heidrich | 7****h | 5 |
| rschwager-hsph | 1****h | 4 |
| George_Weingart | G****t@l****t | 4 |
| Alex Huebner | a****r@g****m | 2 |
| Gholamali Rahnavard | g****i | 2 |
| Jiajie Pu | j****u@f****m | 2 |
| xiestcn | x****n@o****m | 1 |
| sarah872 | s****e@g****t | 1 |
| sagun | s****0@h****m | 1 |
| Robert Stewart | r****t@c****g | 1 |
| Paweł Konieczny | p****y@i****m | 1 |
| Matthias Scholz | m****z@n****g | 1 |
| Florian Plaza Oñate | f****a | 1 |
| Florian Plaza O?ate | f****e@e****m | 1 |
| Gavin John | 1 | |
| Bérénice Batut | b****t@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 100
- Total pull requests: 22
- Average time to close issues: about 1 month
- Average time to close pull requests: about 1 month
- Total issue authors: 90
- Total pull request authors: 15
- Average comments per issue: 2.59
- Average comments per pull request: 0.82
- Merged pull requests: 15
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 5
- Average time to close issues: less than a minute
- Average time to close pull requests: 3 months
- Issue authors: 2
- Pull request authors: 4
- Average comments per issue: 1.0
- Average comments per pull request: 0.8
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- nick-youngblut (4)
- fbeghini (2)
- DarioS (2)
- Caelyn996 (2)
- TKsh6 (2)
- wyx1999 (2)
- alexhbnr (2)
- MGI-EU (2)
- flannsmith (2)
- SMetagenomics (1)
- zhixingfeng (1)
- sjaenick (1)
- javad30 (1)
- JustinGibbons (1)
- Xugh1 (1)
Pull Request Authors
- ljmciver (6)
- ProsperP (4)
- Pandapip1 (3)
- bernt-matthias (2)
- heloint (2)
- HarishChavre (2)
- bebatut (1)
- pkonieczny (1)
- fbeghini (1)
- sixvable (1)
- xiestcn (1)
- kdm9 (1)
- azufre451 (1)
- fplaza (1)
- PuncocharM (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 853 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 29
- Total maintainers: 2
pypi.org: metaphlan
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.
- Homepage: http://github.com/biobakery/MetaPhlAn/
- Documentation: https://metaphlan.readthedocs.io/
- License: LICENSE.txt
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Latest release: 4.2.2
published 9 months ago
Rankings
Dependencies
- biom-format *
- biopython *
- cmseq *
- dendropy *
- h5py *
- numpy *
- pandas *
- phylophlan *
- pysam *
- requests *
- scipy *
- peter-evans/close-issue v1 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- actions/checkout v2 composite
- actions/setup-python v1 composite
- R >= 2.5 depends
- methods * depends