GobyWeb

GobyWeb provides management and analysis of high-throughput sequencing (HTS) data for quantification of gene expression, estimation of DNA methylation, and detection of pathogens.

Key Features:

• Integrated analysis support: Quantification of gene expression from mRNA and small RNA sequencing, estimation of DNA methylation from reduced bisulfite sequencing and whole-genome methyl-seq, and detection of pathogens from sequencing datasets.
• Efficient data management: Engineered to handle large-scale HTS data with a reduced storage footprint compared to traditional analysis pipelines.
• Parallel grid computing: Leverages parallel processing and grid computing to perform analyses rapidly and scale to tens or hundreds of multi-gigabyte samples.
• Performance and scalability: Performance evaluations indicate it matches or outperforms specialized analysis programs in computational efficiency.
• Extensible plugin mechanism: Supports a plugin extension mechanism for adding custom analysis modules.

Scientific Applications:

• Gene expression analysis: Quantification of transcript abundance from mRNA-seq and small RNA-seq experiments.
• Epigenetic profiling: Estimation and analysis of DNA methylation from reduced bisulfite sequencing and whole-genome methyl-seq data.
• Pathogen detection: Identification of pathogens present within sequencing datasets.
• Large-scale genomics/transcriptomics: Processing and analysis of tens to hundreds of multi-gigabyte HTS samples for genomic and transcriptomic studies.

Methodology:

Parallel grid computing and parallel processing combined with storage-efficient data management to accelerate HTS analyses.