PhIP-Seq Analysis Pipeline ONT

Contents:

• Overview
  • Key Features
  • Key Outputs
  • Directory Structure
• Pipeline Architecture
• Installation
  • Prerequisites
  • Setup
• Input Requirements
  • Sample Table
  • Peptide Table
  • Sequencing Data
  • Optional Input Files
• Data Processing
  • Main Workflow
  • 1. Alignment Workflow (ALIGN)
  • 2. Statistics Workflow (STATS)
  • 3. Output Workflow (DSOUT)
  • 4. FHIR Report Workflow (FHIR)
  • 5. FDR Workflow (FDR)
  • 6. Virus Score Workflow (VIRUSSCORE)
  • 7. IEDB Annotation Workflow (IEDB)
  • 8. Visualization Workflow (VISUALIZE)
  • 9. Streamlit Dashboard Workflow (STREAMLIT)
  • 10. Neutralization Prediction Workflow (NEUTRALIZATION_PREDICTION)
  • Workflow Parameters
• Output Files
  • Wide Data Outputs
  • Virus Scores
  • FHIR Output
  • IEDB Annotation Outputs
  • Neutralization Prediction Outputs
  • Visualization Outputs
  • Streamlit Dashboard
• FHIR Standards
  • Profiles Used
  • Standard Terminologies
  • Example: Observation Resource
• Version
  • Pipeline Version
  • Software Dependencies
  • Reference Data
  • References