METAREP specifications

Information


Unique identifier OMICS_01480
Name METAREP
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.4.0
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline METAREP Team <>
  • person_outline Shibu Yooseph <>

Additional information


http://www.youtube.com/watch?v=7FPJaPyLjMk&feature=relmfu http://www.youtube.com/watch?v=j0rlTIkvfvI

Information


Unique identifier OMICS_01480
Name METAREP
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Javascript, Perl, PHP
License MIT License
Computer skills Medium
Version 1.4.0
Stability Beta
Maintained Yes

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Documentation


Maintainers


  • person_outline METAREP Team <>
  • person_outline Shibu Yooseph <>

Additional information


http://www.youtube.com/watch?v=7FPJaPyLjMk&feature=relmfu http://www.youtube.com/watch?v=j0rlTIkvfvI

Publications for METAREP

METAREP in publications

 (15)
PMCID: 5183598
PMID: 28028548
DOI: 10.1128/mSystems.00139-16

[…] associated with the lichen under study. bacterial taxa are presented at the phylum level, and fungal taxa are presented at the species level. taxonomic annotation of genes was performed using the metarep web tool. download figure┬ás1, eps file, 0.8 mb., taxonomic predictions were derived from assembled metagenome annotations and relative gene counts by using the jcvi-supported metarep analysis […]

PMCID: 4990276
PMID: 27536963
DOI: 10.1371/journal.pone.0161292

[…] is of great interest. megan is one of the more well-known software options for metagenomic analysis and visualization of sequence comparison results, as are some web-based platforms such as mg-rast, metarep, and krona [,,,]. the fundamentals of traditional techniques such as heat maps and dendrograms are at the root of all these recent software advances, where hierarchy and relative abundance […]

PMCID: 4869604
PMID: 27199545
DOI: 10.4137/EBO.S36436

[…] wms data, a methodology called humann was developed for inferring the functional and metabolic potential of a microbial community., alternatively, other existing tools, such as img/m, camera, metarep, megan, and comet, can also be used to obtain functional profiles of microbiomes. img/m, metarep, and comet provide a web-based user interface, while camera aims to offer a state-of-the-art […]

PMCID: 4678774
PMID: 26607677
DOI: 10.1016/j.gpb.2015.10.002

[…] to newcomers to the field of metagenomics. it describes 12 online resources and ranks them according to their citations, showing that the most widely used tool is mg-rast, followed by img-m and metarep., antunes et al. looked into the viral communities present in the deep-sea brines of the red sea. these unusual extreme environments have been the targets of several recent studies aiming […]

PMCID: 4678780
PMID: 26602607
DOI: 10.1016/j.gpb.2015.10.003

[…] samples in img . img/m attracts increasing number of researchers due to its in-depth descriptive analyses of metagenomes and genome extraction through binning of metagenomes., metagenomics reports (metarep) is openly available software for comparative metagenomics analysis. it is a well-known open browser for annotation, analysis, and comparison of short reads or assemblies of metagenomics data […]


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METAREP institution(s)
The J Craig Venter Institute, Chinakville, MD, USA
METAREP funding source(s)
Supported by US Department of Energy (#DE-FG02-02ER63453, #DE-FC02-02ER63446); National Institute of Allergy and Infectious Diseases (1U54AI084844); National Cancer Institute (UH2CA14023); Sloan Foundation (#2004-5-46EG); University of Illinois, Department of Primary Industries, Victoria, Australia.

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