BugBase specifications

Information


Unique identifier OMICS_18109
Name BugBase
Interface Web user interface
Restrictions to use None
Input data An OTU table or an image.
Input format TXT or BIOM or WGS.Basic
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Dan Knights <>

Information


Unique identifier OMICS_18109
Name BugBase
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An OTU table or an image.
Input format TXT or BIOM or WGS.
Operating system Unix/Linux, Mac OS
Programming languages R
Computer skills Advanced
Stability Stable
Requirements
Ape, optparse, beeswarm, RColorBrewer, reshape2, plyr, grid, gridExtra, ggplot2, biom
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Dan Knights <>

Publication for BugBase

BugBase in publications

 (3)
PMCID: 5900040
PMID: 29686662
DOI: 10.3389/fmicb.2018.00699

[…] out, and the bacterial and fungal otu tables were subsampled to 14,000 and 24,000 sequences per sample, respectively, for further analysis. phenotypes of bacterial communities were predicted using bugbase (ward et al., unpublished)., multiple co-inertia analysis (mcia) () was performed to identify the changing trends of microbial communities in different tillage treatments and soil layers. […]

PMCID: 5636226
PMID: 29034327
DOI: 10.1128/mSphere.00351-17

[…] of fungal taxonomy calling, and variability in functions expressed by fungi depending on specific environmental conditions, compared to bacterial sequences. nevertheless, we were able to use bugbase () to infer bacterial community functions of mouse gut microbiomes in order to identify potential links between fungi and metabolic potential of gut bacterial microbiomes. of a total of 558 […]

PMCID: 5145865
PMID: 28018861
DOI: 10.3389/fcimb.2016.00179

[…] were closed-reference picked at 97% identity using uclust_ref (edgar, ) and the green genes core set (version 13.5). the resulting otu table was rarefied to 13,944 sequences and submitted to bugbase (http://github.com/danknights/bugbase) in order to calculate differences between both groups in terms of microbial phenotypes., we detected and quantified the absolute number of 16s rrna b. […]


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BugBase institution(s)
Biotechnology Institute, University of Minnesota, Minneapolis, MN, USA; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA; Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA; Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA; Department of Computer of Science, University of California San Diego, San Diego, CA, USA; Department of Pediatrics, University of California San Diego, San Diego, CA, USA; Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA; Department of Biology, St Cloud State University, St. Cloud, MN, USA; Food Science and Nutrition, University of Minnesota, Saint Paul, MN, USA
BugBase funding source(s)
Supported by the National Institutes of Health (NIH), AI121383-01A1, and the Minnesota Partnership Grant Program, 13.28.

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