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GobyWeb: Web Application for Next-generation Sequencing Data Alignment and Analysis

Detailed Technology Description

A high-throughput web-based application was developed that helps even non-technical users to process large amounts of next-generation sequencing data.

Others

• Kevin C. Dorff, Nyasha Chambwe, Zachary Zeno, Manuele Simi, Rita Shaknovich, and Fabien Campagne. GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. PLOS One,2013.

• List of published studies where GobyWeb was used for analysis: http://campagnelab.org/software/gobyweb/cited-by/

• GobyWeb can be obtained at http://gobyweb.campagnelab.org and is freely available for non-commercial use. GobyWeb plugins are distributed in source code and licensed under the open source LGPL3 license to facilitate code inspection, reuse and independent extensions http://github.com/CampagneLaboratory/gob​yweb2-plugins.

*Abstract

The system, GobyWeb, aligns short read sequences to reference genomes or transcriptomes, produces alignment files in the Goby compact form, and conducts tests of significance for differential expression studies with RNA sequence data. 

 

GobyWeb operates by leveraging alignment tools developed in the research community to split very large read files in pieces and align each piece on a cluster.  Using this method GobyWeb is able to align 100 million 10bp reads in two hours on a moderately-sized cluster.  The resulting alignments are automatically post-processed to generate Goby counts and wiggle plots for visualization in genome viewers such as UCSC, IGV, etc.).  Users can specify which information to download to their computers for further processing with the open-source Goby framework, which offers several programs for RNA-seq data analysis.

 

Potential Applications 

• Large-scale alignment of next-generation sequencing data (high-throughput sequencing), e.g.:
  • quantification of gene expression for messenger and small RNA sequencing
  • estimation of DNA methylation (i.e., reduced bisulfite sequencing and whole genome methyl-seq)
  • detection of pathogens in sequenced data
• Generating wiggle tracks for visualization in genome viewers
• Differential expression studies across groups
• Mapping to the transcriptome or to a full genome

 

Advantages

• Enables non-technical users with minimal training to process large amounts of sequencing data
• Provides alignments in a format suitable for efficient custom downstream analysis and using tools available via open-source licenses
• Scaleable, high-throughput method

*Licensing

Martin Teschlmt439@cornell.edu(607) 254-4454

Country/Region

USA