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. 2009 Dec 18:10:430.
doi: 10.1186/1471-2105-10-430.

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads

Wolfgang Gerlach  1 , Sebastian Jünemann, Felix Tille, Alexander Goesmann, Jens Stoye
Affiliations

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads

Wolfgang Gerlach et al. BMC Bioinformatics. .

Abstract

Background: Metagenomics is a new field of research on natural microbial communities. High-throughput sequencing techniques like 454 or Solexa-Illumina promise new possibilities as they are able to produce huge amounts of data in much shorter time and with less efforts and costs than the traditional Sanger technique. But the data produced comes in even shorter reads (35-100 basepairs with Illumina, 100-500 basepairs with 454-sequencing). CARMA is a new software pipeline for the characterisation of species composition and the genetic potential of microbial samples using short, unassembled reads.

Results: In this paper, we introduce WebCARMA, a refined version of CARMA available as a web application for the taxonomic and functional classification of unassembled (ultra-)short reads from metagenomic communities. In addition, we have analysed the applicability of ultra-short reads in metagenomics.

Conclusions: We show that unassembled reads as short as 35 bp can be used for the taxonomic classification of a metagenome. The web application is freely available at http://webcarma.cebitec.uni-bielefeld.de.

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Figures

Figure 1
Figure 1
Overview WebCARMA. The web application WebCARMA.
Figure 2
Figure 2
Functional Profile. Example of a functional profile: 40 most abundant GO-terms in the metagenome of an agricultural biogas reactor.
Figure 3
Figure 3
EGT lengths distribution. EGT length distribution in each data set as a function of read length. Shown are the minimum, 25% quantile, median, 75% quantile and maximum.
Figure 4
Figure 4
superkingdom. Taxonomic results on the level of superkingdom.
Figure 5
Figure 5
order. Taxonomic results on the level of order. Only taxa with an abundance of 0.015 or higher are shown.
Figure 6
Figure 6
species. Taxonomic results on the level of species. Only taxa with an abundance of 0.015 or higher are shown.
See this image and copyright information in PMC

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