SEQprocess

SEQprocess processes Next-Generation Sequencing (NGS) data as an R package, providing modular, reproducible pipelines — including GATK for variant calling, TopHat2/Cufflink for RNA abundance, and Sequenza for DNA copy number — and exports results as ExpressionSet or SummarizedExperiment.

Key Features:

• Modular Design: Fully modularized processing steps that can be configured into custom pipelines for different NGS applications.
• Pre-configured Pipelines: Six pre-configured pipelines for common tasks including variant calling, allele frequency estimation, RNA abundance analysis, and DNA copy number assessment.
• Tool Integrations: Integrates established tools and algorithms such as GATK, TopHat2, Cufflink, and Sequenza for specific analyses.
• Clinical Sequencing Support: Includes pipelines tailored for clinical data types such as cell-free DNA and miR-Seq.
• R Integration: Converts processed NGS data into R-compatible formats, including ExpressionSet and SummarizedExperiment.
• Reproducibility and Reporting: Generates automated reports summarizing each processing step to support reproducibility.
• Extensibility: Framework supports incorporation of additional tools or modification of existing pipelines as methods evolve.
• GDC Compatibility: Provides compatibility with established pipelines such as those from the National Cancer Institute's Genomic Data Commons (GDC).

Scientific Applications:

• Variant Calling and Allele Frequency Estimation: Detection of sequence variants and estimation of allele frequencies using GATK and related procedures.
• RNA Abundance Quantification: RNA-seq expression analysis using TopHat2 and Cufflink for transcript abundance estimation.
• DNA Copy Number Assessment: DNA copy number analysis using Sequenza.
• Clinical and Cancer Genomics: Processing of clinical sequencing data including cell-free DNA and miR-Seq for cancer research and diagnostics.
• Integration with GDC Workflows: Use in cancer genomics studies that integrate with Genomic Data Commons pipelines.

Methodology:

Modularized pipeline framework with six pre-configured pipelines; variant calling using GATK; allele frequency estimation; RNA abundance analysis using TopHat2 and Cufflink; DNA copy number analysis using Sequenza; conversion of outputs to ExpressionSet or SummarizedExperiment; automated report generation.