GRAPEVNE

GRAPEVNE streamlines the creation, execution, and sharing of modular analytical pipelines for infectious disease data analysis through an intuitive graphical interface built on the Snakemake workflow management system.

Key Features:

• Modular Pipeline Construction: Each module is a self-contained Snakemake workflow complete with configurations, scripts, and metadata, enabling interoperability between components.
• Graphical Workflow Design: Provides a visual interface for building complex and repetitive data analysis workflows without requiring direct command-line interaction with Snakemake.
• Workflow Execution and Sharing: Supports the creation, execution, and distribution of analytical pipelines to enhance reproducibility in computational research.
• Open-Source Architecture: Enables community-driven development and scalability of pipeline modules and core functionality.

Scientific Applications:

• Genomic Analysis: Supports automated phylogenetic analysis of viral sequences and other genomic data processing workflows.
• Epidemiological Modeling: Enables real-time outbreak monitoring, forecasting, and processing of epidemiological data.
• Phylogeographic Inference: Demonstrated through end-to-end automation from sequence retrieval to phylogeographic inference, as shown in the dengue virus pipeline.
• Large-Scale Data Processing: Handles complex and repetitive data analysis workflows across diverse data types including clinical, genomic, epidemiological, and spatial data.

Methodology:

GRAPEVNE is built on the Snakemake workflow management system, where each module is implemented as a self-contained Snakemake workflow with configurations, scripts, and metadata. Pipelines are constructed graphically by connecting these modular components.