Large scale metagenomics statistics

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Large scale metagenomics specifications


Unique identifier OMICS_11535
Name Large scale metagenomics
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes


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  • person_outline Pierre Mahé <>

Publication for Large scale metagenomics

Large scale metagenomics in publications

PMCID: 5610413
PMID: 28938903
DOI: 10.1186/s40168-017-0339-6

[…] luteus, and kocuria rhizophila have been identified as “signature microbes” of healthcare settings, including the neonatal intensive care unit and hospital air samples []. additionally, a recent large-scale metagenomics hospital study, has also found an abundance of staphylococcus and propionibacterium and has similarly found a preponderance of skin associated microbes on surfaces []., […]

PMCID: 5397404
PMID: 28473812
DOI: 10.3389/fmicb.2017.00666

[…] gh33 (sialidases and other ulosonic acid hydrolases), gh25 (lysozymes). interestingly, the relative abundance of enzymes that target cellulose and xylan is lower than what was found in a large scale metagenomics investigation of the cow rumen (hess et al., ; table )., taken from hess et al. ()., this work; average of large intestine and rectum for the three animals, scaled […]

PMCID: 5099504
PMID: 27877158
DOI: 10.3389/fmicb.2016.01740

[…] the fact that only a minority of bacterial hosts can be cultivated in laboratories (edwards and rohwer, ) make the assessment of such heterogeneity very challenging. although, culture-independent, large-scale metagenomics has paved the way to a more exhaustive understanding of the viral sequence space (dutilh, ), this approach is not flawless. for example, small datasets may be obtained due […]

PMCID: 4052219
PMID: 24966863
DOI: 10.3389/fpls.2014.00268

[…] components of the phytobiome in their analyses. to this end, we consider here approaches based on next generation sequencing (ngs) to detect microbial components of the phytobiome. ngs has enabled large-scale metagenomics, which is a gene-based study of all organisms associated with a particular sample (; ). time-efficient and -effective means of examining ngs databases to identify organisms […]

PMCID: 3742672
PMID: 23967117
DOI: 10.1371/journal.pone.0070837

[…] the phylogenetic relations among microbial species –. the 16s rrna based phylogenetic inference has revolutionized our view of microbial diversity and composition of many environments –. many large-scale metagenomics projects have been undertaken to investigate various aspects of the microbial composition, e.g. human microbiome project (, international census […]

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Large scale metagenomics institution(s)
Bioinformatics Research Departement, bioMérieux, Marcy-l’Étoile, France; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Fontainebleau, France; Institut Curie, Paris, France; INSERM U900, Paris, France
Large scale metagenomics funding source(s)
This work was supported by the European Research Council (SMAC-ERC-280032) and the French National Research Agency (ANR-11-BINF-0001).

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