Software
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
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* Corresponding author: Wolfgang Gerlach wolfgang.gerlach@cebitec.uni-bielefeld.de
1 Faculty of Technology, Bielefeld University, Bielefeld, Germany
2 Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
3 Department of Periodontology, University Hospital Münster, Münster, Germany
BMC Bioinformatics 2009, 10:430 doi:10.1186/1471-2105-10-430
Published: 18 December 2009Abstract
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 webcite.