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Published 2017

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Publication details

Journal : BMC Bioinformatics , vol. 18 , p. 9 , 2017

Publisher : BioMed Central (BMC)

International Standard Numbers :
Printed : 1471-2105
Electronic : 1471-2105

Publication type : Academic article

Contributors : Liland, Kristian Hovde; Vinje, Hilde; Snipen, Lars-Gustav

Issue : 172

If you have questions about the publication, you may contact Nofima’s Chief Librarian.

Kjetil Aune
Chief Librarian
kjetil.aune@nofima.no

Summary

Background

Taxonomic classification based on the 16S rRNA gene sequence is important for the profiling of microbial communities. In addition to giving the best possible accuracy, it is also important to quantify uncertainties in the classifications.


Results

We present an R package with tools for making such classifications, where the heavy computations are implemented in C++ but operated through the standard R interface. The user may train classifiers based on specialized data sets, but we also supply a ready-to-use function trained on a comprehensive training data set designed specifically for this purpose. This tool also includes some novel ways to quantify uncertainties in the classifications.


Conclusions

Based on input sequences of varying length and quality, we demonstrate how the output from the classifications can be used to obtain high quality taxonomic assignments from 16S sequences within the R computing environment. The package is publicly available at the Comprehensive R Archive Network.