METAGENassist protocols

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METAGENassist specifications

Information


Unique identifier OMICS_07815
Name METAGENassist
Interface Web user interface
Restrictions to use None
Input format Users upload a taxonomic profile in one of several supported formats. A taxonomic profile file contains the names of microbial species (or other taxonomic classes) and their relative abundance in at least 2 samples. Accepted formats include CSV format, or data generated by mothur, QIIME, MG-RAST, MEGAN, and STAMP. Users will also benefit by uploading an optional file containing metadata for each sample (CSV format).
Output format Upon completion, METAGENassist generates a variety of well-annotated tables and colorful, labeled graphs in an anti-aliased PNG format. PDF versions for some plots are also available. The processed data and images are available for download.
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/METAGENassist

Maintainer


  • person_outline David Wishart <>

Publication for METAGENassist

METAGENassist in pipelines

 (3)
2017
PMCID: 5522462
PMID: 28733590
DOI: 10.1038/s41598-017-06232-w

[…] to closed-reference otu-picking compared to using all the available read data for each study. taxonomic-to-phenotypic mapping was performed by linking otus nomenclature to taxonomic assignments in metagenassist. the graphical representation of the phenotipic cladogram was constructed with graphlan software., all sequence data are available through the national center for biotechnology […]

2016
PMCID: 5123330
PMID: 27884207
DOI: 10.1186/s13073-016-0368-y

[…] sequence reads (17,657–828,181 reads per sample) were obtained (mean of 199,591 ± 190,153 reads) after quality control. further processing for visualization was performed using qiime [] and metagenassist []., to compare the microbiota composition between cohorts, we summarized the data using both α-diversity and β-diversity. α-diversity reflects species richness and evenness within […]

2015
PMCID: 4592952
PMID: 26434367
DOI: 10.1038/srep14603

[…] were aligned, clustered, and operational taxonomic units (otus) were determined utilizing the greengenes reference collection (greengenes.lbl.gov). principal component analysis was performed using metagenassist. alpha and beta diversity were evaluated using qiime and the megan open source software package. student’s t-tests were used to identify taxa that displayed statistically significant […]


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METAGENassist in publications

 (23)
PMCID: 5894178
PMID: 29636083
DOI: 10.1186/s13567-018-0530-1

[…] dissimilarity index. differences in functional profiles of gastric bacterial communities were analyzed by mapping taxa into several phenotypes (i.e. metabolism, gram staining, sporulation,…) using metagenassist® []. only the phenotypes detected in more than 50% of the samples were included for further analysis., statistical analysis was performed using spss statistics 24® (ibm, new york, usa). […]

PMCID: 5758573
PMID: 29311639
DOI: 10.1038/s41598-017-18461-0

[…] phylogenetic trees were based on the reference sequences and the kogelberg biosphere reserve virome sequences, and computed with 100 bootstraps. further analysis of the sequences was performed using metagenassist (a web server that provides a broad range of statistical tools for comparative metagenomics). functional assignments produced by virome using 120 identified functional subsystems […]

PMCID: 5522462
PMID: 28733590
DOI: 10.1038/s41598-017-06232-w

[…] to closed-reference otu-picking compared to using all the available read data for each study. taxonomic-to-phenotypic mapping was performed by linking otus nomenclature to taxonomic assignments in metagenassist. the graphical representation of the phenotipic cladogram was constructed with graphlan software., all sequence data are available through the national center for biotechnology […]

PMCID: 5431125
PMID: 28469129
DOI: 10.1038/s41598-017-01202-8

[…] to identify the pathways affected in the sub groups of gbm patients., itraq data for the tissue proteomic analysis of svz−, svz+ gbm tumors and normal/control tissues was subjected to plsda using metagenassist, an online tool. both svz− and svz+ gbms were segregated from each other on a 3d-score plot obtained from this multivariate analysis., hemopexin levels in gbm patient (both svz+ […]

PMCID: 5374439
PMID: 28361923
DOI: 10.1038/srep45362

[…] when the ratio of mean sequence counts in mucus over water samples was <1., functional differences based on bacterial 16s community composition (otu taxonomy and abundance), were assessed with metagenassist. input files were created in mothur using the ‘make.shared’ and ‘classify.otu’ commands based on all coral samples. 1,978 distinct otus were assigned, mapped, condensed into 500 […]


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METAGENassist institution(s)
Department of Computing Science, University of Alberta, Edmonton, AB, Canada

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