WebMGA: a customizable web server for fast metagenomic sequence analysis

BMC Genomics

Software

Sitao Wu¹  Weizhong Li¹  Liming Fu¹  Beifang Niu¹  Zhengwei Zhu¹ 

[1] Center for Research in Biological Systems, University of California San Diego, 92093, La Jolla, California, USA;

关键词: FASTA Format;    Pathway Annotation;    FASTQ Format;    Metagenomic Sequence Data;    Daemon Process;   

DOI  :  10.1186/1471-2164-12-444

 received in 2011-05-12, accepted in 2011-09-07,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundThe new field of metagenomics studies microorganism communities by culture-independent sequencing. With the advances in next-generation sequencing techniques, researchers are facing tremendous challenges in metagenomic data analysis due to huge quantity and high complexity of sequence data. Analyzing large datasets is extremely time-consuming; also metagenomic annotation involves a wide range of computational tools, which are difficult to be installed and maintained by common users. The tools provided by the few available web servers are also limited and have various constraints such as login requirement, long waiting time, inability to configure pipelines etc.ResultsWe developed WebMGA, a customizable web server for fast metagenomic analysis. WebMGA includes over 20 commonly used tools such as ORF calling, sequence clustering, quality control of raw reads, removal of sequencing artifacts and contaminations, taxonomic analysis, functional annotation etc. WebMGA provides users with rapid metagenomic data analysis using fast and effective tools, which have been implemented to run in parallel on our local computer cluster. Users can access WebMGA through web browsers or programming scripts to perform individual analysis or to configure and run customized pipelines. WebMGA is freely available at http://weizhongli-lab.org/metagenomic-analysis.ConclusionsWebMGA offers to researchers many fast and unique tools and great flexibility for complex metagenomic data analysis.

【 授权许可】

Unknown   
© Wu et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.