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

被引：46

作者：

Gerlach, Wolfgang ^{[1
,2
]}

Juenemann, Sebastian ^{[2
,3
]}

Tille, Felix ^{[2
]}

Goesmann, Alexander ^{[2
]}

Stoye, Jens ^{[1
,2
]}

机构：

[1] Univ Bielefeld, Fac Technol, Bielefeld, Germany

[2] Univ Bielefeld, Ctr Biotechnol CeBiTec, Bielefeld, Germany

[3] Univ Hosp Munster, Dept Periodontol, Munster, Germany

来源：

BMC BIOINFORMATICS | 2009年 / 10卷

关键词：

PHYLOGENETIC CLASSIFICATION; MICROBIAL COMMUNITY; IDENTIFICATION; GENOMES; BIASES;

D O I：

10.1186/1471-2105-10-430

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页数：10

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