Pathogen Analysis System (PAS): A scalable genomic data processing framework integrated with the European Nucleotide Archive

The Pathogen Data Network (PDN) consists of two interconnected networks: local private data hubs for public health and global public knowledge bases for genomic research. The Pathogen Analysis System (PAS) in PDN is a computing platform to process pathogen data by integrating with the European Nucleotide Archive (ENA). PAS retrieves input data from ENA, processes it using customizable bioinformatics pipelines, and submits results back to ENA, which may then be highlighted in a Pathogens Portal.PAS supports four use cases:1. Public data on PDN’s priority list (ENA-sourced).2. Public data not on the priority list (ENA-sourced).3. Private data stored in ENA.4. Data uploaded directly to Galaxy Community Hub, bypassing ENA.The system leverages tools like the ENA File Downloader and Webin CLI for Submission, wrapped as Galaxy tools, to automate workflows. A reference implementation using the Tuberculosis (TB) Variant Analysis Workflow demonstrates how researchers can retrieve data, analyze it, and submit results seamlessly.Developed in collaboration with GA4GH, ENA, EVORA, and BRC Analytics, PAS operates on a layered architecture, enabling scalable, automated analysis. Researchers can plug in their own pipelines or reuse existing ones, benefiting from Galaxy’s computing power without manual data handling.While UC1 is pathogen-specific, UC2-UC4 are generic, making PAS adaptable for any genomic data analysis integrated with ENA. The system also aligns with FAIR principles, with plans to share workflows via WorkflowHub and package them in RO-Crates for improved reproducibility and accessibility. This framework enhances collaborative research, enabling rapid data sharing and analysis.