Methods for comparative metagenomics

Daniel H Huson,Alexander F Auch,Daniel C Richter,Suparna Mitra,Stephan C Schuster

doi:10.1186/1471-2105-10-s1-s12

Daniel H Huson, Alexander F Auch + Show 3 more

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https://doi.org/10.1186/1471-2105-10-s1-s12

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Abstract

BackgroundMetagenomics is a rapidly growing field of research that aims at studying uncultured organisms to understand the true diversity of microbes, their functions, cooperation and evolution, in environments such as soil, water, ancient remains of animals, or the digestive system of animals and humans. The recent development of ultra-high throughput sequencing technologies, which do not require cloning or PCR amplification, and can produce huge numbers of DNA reads at an affordable cost, has boosted the number and scope of metagenomic sequencing projects. Increasingly, there is a need for new ways of comparing multiple metagenomics datasets, and for fast and user-friendly implementations of such approaches.ResultsThis paper introduces a number of new methods for interactively exploring, analyzing and comparing multiple metagenomic datasets, which will be made freely available in a new, comparative version 2.0 of the stand-alone metagenome analysis tool MEGAN.ConclusionThere is a great need for powerful and user-friendly tools for comparative analysis of metagenomic data and MEGAN 2.0 will help to fill this gap.

Highlights

Metagenomics is a rapidly growing field of research that aims at studying uncultured organisms to understand the true diversity of microbes, their functions, cooperation and evolution, in environments such as soil, water, ancient remains of animals, or the digestive system of animals and humans
BMC Bioinformatics 2009, 10(Suppl 1):S12 http://www.biomedcentral.com/1471-2105/10/S1/S12 technologies [1,2], which do not require cloning or PCR amplification, and can produce huge numbers of DNA reads at an affordable cost, has boosted the number and scope of metagenomic sequencing projects, see [3,4]
In this paper we have discussed a number of new techniques that address this issue. These will all be made available in a new version 2.0 of MEGAN

Summary

Introduction

Metagenomics is a rapidly growing field of research that aims at studying uncultured organisms to understand the true diversity of microbes, their functions, cooperation and evolution, in environments such as soil, water, ancient remains of animals, or the digestive system of animals and humans. BMC Bioinformatics 2009, 10(Suppl 1):S12 http://www.biomedcentral.com/1471-2105/10/S1/S12 technologies [1,2], which do not require cloning or PCR amplification, and can produce huge numbers of DNA reads at an affordable cost, has boosted the number and scope of metagenomic sequencing projects, see [3,4]. The analysis of such datasets is aimed at determining and comparing the biological diversity and the functional activity of different microbial communities

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Conclusion