SePIA

SePIA provides a standardized computational workflow for processing, integrating, and analyzing large-scale RNA sequencing data, including small RNA and complementary RNA datasets, to enable consistent downstream interpretation.

Key Features:

• Comprehensive workflow architecture: A dynamic pipeline architecture capable of individually analyzing and integrating small RNA and RNA data to ensure consistency across processing stages.
• Integration with established tools: Supports execution of over 20 commonly used RNA-seq tools via an established workflow engine.
• Docker-based containerization: Implemented using Docker to provide reproducible execution environments.
• Resource management: The underlying pipeline engine supports computational resource management to optimize performance.
• Modular design for customization: Modular components allow workflows to be customized for specific experimental needs while preserving overall structure.
• HTML reporting: Analysis results are organized into a comprehensive HTML report.

Scientific Applications:

• Small RNA and complementary RNA studies: Processing and integration of small RNA and complementary RNA datasets for downstream analysis.
• Breast cancer RNA-seq analysis: Applied to analyses of three breast cancer datasets to extract biological insights from complex sequencing data.

Methodology:

SePIA executes over 20 RNA-seq tools using an established workflow engine, is implemented with Docker containers, uses a pipeline engine for computational resource management, and produces a comprehensive HTML report.