MetaPhlAn pipeline

MetaPhlAn specifications

Information


Unique identifier OMICS_02286
Name MetaPhlAn
Alternative names Metagenomic Phylogenetic Analysis, MetaPhlAn2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Shotgun metagenome sequencing results.
Input format FASTQ, SAM
Output data Table of microbial species and their relative abundance for each input.
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Version 2
Stability Stable
Requirements Python, Bowtie, Numpy, Pandas, BioPython, SciPy, Matplotlib, biom
Maintained Yes

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Documentation


Maintainers


  • person_outline Nicola Segata <>
  • person_outline Duy Tin Truong <>

Additional information


http://huttenhower.sph.harvard.edu/metaphlan

Publications for Metagenomic Phylogenetic Analysis

MetaPhlAn IN pipelines

 (17)
2018
PMCID: 5859664
PMID: 29554948
DOI: 10.1186/s40168-018-0437-0

[…] r2 = 0.011), but there was a significant difference between the results predicted by the species classifiers (p = 0.01, r2 = 0.127). the relative abundances predicted by the classifiers, apart from metaphlan2, were apparently biased by reference genome sizes. additionally, we observed varying false-positive rates among the classifiers. metaphlan2 had the lowest false-positive rate, whereas […]

2018
PMCID: 5859664
PMID: 29554948
DOI: 10.1186/s40168-018-0437-0

[…] abundances predicted by the classifiers, apart from metaphlan2, were apparently biased by reference genome sizes. additionally, we observed varying false-positive rates among the classifiers. metaphlan2 had the lowest false-positive rate, whereas slimm had the greatest false-positive rate. strain-level analysis results were also similar across platforms. each platform correctly identified […]

2017
PMCID: 5310281
PMID: 28198672
DOI: 10.1186/s12864-016-3254-5

[…] to merge pair-ended reads where paired reads were removed if their overlaps were over 65 bp., a total of 43 metagenomes sampled from healthy and periodontitis subgingival plaques were analyzed using metaphlan [26], which mapped metagenomic reads to a marker gene catalogue and identified oral microbiota species inhabiting sample environments based on all available reference genomes […]

2017
PMCID: 5310281
PMID: 28198672
DOI: 10.1186/s12864-016-3254-5

[…] to estimate the relative abundance of microbes present in the oral sample as identified in the expanded phylogenetic analysis. the complete genomes of present archaea and bacteria, as detected by metaphlan, were downloaded from the human oral microbiome database [29] to construct the refined reference set for grammy analysis. bwa-mem [30] was used to align those metagenomic reads that passed […]

2017
PMCID: 5310281
PMID: 28198672
DOI: 10.1186/s12864-016-3254-5

[…] preprocessing, in which tagcleaner, prinseq, deconseq and flash [22–25] were used to remove low quality reads and contamination from the human genome; (2) expanded phylogenetic analysis, in which metaphlan [26] was used to sensitively detect the presence of microbial species inoral samples; (3) refined phylogenetic analysis, in which grammy [27] was used to accurately estimate the relative […]

MetaPhlAn institution(s)
Centre for Integrative Biology, University of Trento, Trento, Italy; Biostatistics Department, Harvard School of Public Health, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
MetaPhlAn funding source(s)
Supported in part by the US National Institutes of Health (grants R01HG005969 and U54DE023798), the US National Science Foundation (grant DBI-1053486), the US Army Research Office (grant W911NF-11-1-0473), Danone Research (grant PLF-5972-GD) the European Union Seventh Framework Programme (Marie Curie grant PCIG13-618833), the Italian Ministry of Education, University and Research (grant FIR RBFR13EWWI), Fondazione Caritro (grant Rif.Int.2013.0239) and Terme di Comano.

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