WebCARMA：一个用于未组装宏基因组读取的功能和分类学分类的网络应用程序。

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

机构信息

Faculty of Technology, Bielefeld University, Bielefeld, Germany.

出版信息

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

DOI:10.1186/1471-2105-10-430

PMID:20021646

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2801688/

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.

摘要

背景

宏基因组学是一个研究自然微生物群落的新领域。高通量测序技术，如 454 或 Solexa-Illumina，具有产生大量数据的新可能性，因为它们比传统的 Sanger 技术能够在更短的时间内以更少的努力和成本产生更多的数据。但是，所产生的数据的读取长度更短（Illumina 的读取长度为 35-100 个碱基，454 测序的读取长度为 100-500 个碱基）。CARMA 是一种新的软件管道，用于使用短的未组装读取来描述微生物样品的物种组成和遗传潜力。