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Bioinformatics Advance Access originally published online on August 20, 2009
Bioinformatics 2009 25(20):2737-2738; doi:10.1093/bioinformatics/btp508
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

Erik Kristiansson 1,2,*, Philip Hugenholtz 3 and Daniel Dalevi 4,*

1Department of Zoology, University of Gothenburg, 2Department of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Göteborg, Sweden, 3Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, USA and 4Department of Computer Science And Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden

* To whom correspondence should be addressed.


  Abstract

Summary: Microorganisms are ubiquitous in nature and constitute intrinsic parts of almost every ecosystem. A culture-independent and powerful way to study microbial communities is metagenomics. In such studies, functional analysis is performed on fragmented genetic material from multiple species in the community. The recent advances in high-throughput sequencing have greatly increased the amount of data in metagenomic projects. At present, there is an urgent need for efficient statistical tools to analyse these data. We have created ShotgunFunctionalizeR, an R-package for functional comparison of metagenomes. The package contains tools for importing, annotating and visualizing metagenomic data produced by shotgun high-throughput sequencing. ShotgunFunctionalizeR contains several statistical procedures for assessing functional differences between samples, both for individual genes and for entire pathways. In addition to standard and previously published methods, we have developed and implemented a novel approach based on a Poisson model. This procedure is highly flexible and thus applicable to a wide range of different experimental designs. We demonstrate the potential of ShotgunFunctionalizeR by performing a regression analysis on metagenomes sampled at multiple depths in the Pacific Ocean.

Availability: http://shotgun.zool.gu.se

Contact: dalevi{at}chalmers.se; erik.kristiansson{at}zool.gu.se

Supplementary information: supplementary data are available at Bioinformatics online.

Associate Editor: Alex Bateman

Received on July 3, 2009; revised on August 16, 2009; accepted on August 17, 2009

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