Platform-agnostic TB genomics pipeline (TBtoFHIR)

Contents:

• Overview
  • Key Features
  • Key Outputs
  • Directory Structure
• Pipeline Architecture
• Installation
  • Prerequisites
  • Setup
  • Usage
• Input Requirements
  • Illumina Reads
  • Nanopore Reads
  • Raw VCFs
• Data Processing
  • Main Workflow
  • Nanopore (Long-Read) Workflow
  • Illumina (Short-Read) Workflow
  • VCF Workflow
  • Variant Annotation
  • Lineage Classification
  • FHIR Converter
  • Upload to FHIR Server
  • Workflow Parameter
• Output Files
  • FHIR Genomic Bundle
  • Clinical Data Integration & Reporting
  • Drug Resistance Classification
  • Output Directory Structure
• FHIR Standards
  • Profiles Used
  • Standard Terminologies
• Version
  • Pipeline Version
  • Software Dependencies
  • Reference Data
  • Changelog
  • References