Platform-agnostic DENV analysis pipeline to FHIR (DENVtoFHIR)

Contents:

• Overview
  • Key Features
  • Key Outputs
  • Directory Structure
• Pipeline Architecture
  • DENV Analysis Diagram
• Installation
  • Prerequisites
  • Setup
• Input Requirements
  • Illumina Reads
  • Nanopore Reads
• Data Processing
  • Main Workflow Controller
  • Pre-processing & Host Removal
  • Serotyping
  • Nanopore (Long-Read) Workflow
  • Illumina (Short-Read) Workflow
  • Genotyping & Variant Analysis
  • Reporting
  • FHIR Converter
  • Upload to FHIR Server
  • Workflow Parameter
• Output Files
  • FHIR Genomic Observations
  • Clinical Data Integration & Reporting
  • Analysis Logic
  • Output Directory Structure
• FHIR Standards
  • Standard Terminologies Used
• Version
  • Pipeline Version
  • Software Dependencies