ScriptManager: a platform for scalable and reproducible high-resolution analysis of genomics datasets.

Area of Science:

• Genomics and Epigenomics
• Computational Biology
• Bioinformatics

Background:

• Diverse genomic and epigenomic assays generate complex data.
• Existing analysis and figure-generation tools are often assay-specific, limiting interoperability and reproducibility.

Purpose of the Study:

• To present ScriptManager v1.0, a Java-based framework for modular and reproducible genomics and epigenomics data analysis and visualization.
• To provide a unified and extensible solution for cross-assay visualization and workflow reproducibility.

Main Methods:

• Developed a Java-based framework (ScriptManager v1.0) with novel analytical modules.
• Integrated GUI session logging, automated testing, tutorials, and expanded documentation.
• Incorporated support for Singularity containers, Anaconda packaging, and Galaxy XML wrappers for enhanced reproducibility.

Main Results:

• ScriptManager v1.0 offers a unified framework for cross-assay visualization and workflow reproducibility.
• Demonstrated scalability of TagPileup analysis from single-core to a 10,305-job distributed analysis on the Open Science Grid (OSG) in under 2 hours.
• Enhanced workflow portability, transparency, and reproducibility for high-resolution genomic assays.

Conclusions:

• ScriptManager v1.0 bridges exploratory data analysis and publication-ready figure generation.
• Facilitates building, sharing, and reproducing genomic analyses across diverse computational infrastructures with minimal configuration.
• Improves the overall reproducibility and transparency of genomic data analysis workflows.