WebMGA: a customizable web server for fast metagenomic sequence analysis
By Sitao Wu, Zhengwei Zhu, Limin Fu, Beifang Niu, Weizhong Li. BMC Genomics, 2011
612 citations recorded by the source corpus.
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.
Subfields: Ecology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/17a7ab7ea67e2e00c7bcc2b80a6e67768142b644
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Ecology
- Weizhong Li
- Shibu Yooseph
- Limin Fu
- Beifang Niu
- Satchidananda Panda
- John C. Wooley
- Amir Zarrinpar
- Sitao Wu
In Molecular Biology
- Sitao Wu
- Beifang Niu
- Limin Fu
- John C. Wooley
- Weizhong Li
- Yang Zhang
- Shibu Yooseph
- Satchidananda Panda
Citations in the corpus
- Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome (2014, positive): “However, longitudinal consistencies in gut-microbiome composition are strongly associated with long-term dietary patterns (Wu et al., 2011a).”
- Ultrafast clustering algorithms for metagenomic sequence analysis (2012, methodology): “It is also available from the cd-hit web server [28], the CAMERA web portal [42] and the WebMGA server [43] for metagenomic data analysis.”
- The Bacterial Community Composition of the Bovine Rumen Detected Using Pyrosequencing of 16S rRNA Genes (2012, methodology): “The consensus sequences of clusters identified using CD-HIT-OTU were then annotated using FR-HIT [29] against the GreenGene database.”