EFSA Pipeline Documentation

Welcome to the EFSA Pipeline documentation. This pipeline provides comprehensive tools for genomic analysis, including quality control, validation, and variant detection.

Quick Navigation

Getting Started

• Quick Start Guide
• Docker Setup

Input Validation

• Validation Overview
• Supported File Formats
• Configuration Guide
• Validation Settings
• Performance Tips

Nextflow Pipeline

• Running the Pipeline
• Methods
• Runtime Messages
• Directory Structures
• Pipeline Visualization

Project Compliance

• Third-Party Licenses

Output Documentation

• Reference vs Modified FASTA Pipeline
• Short-Read Pipeline (Illumina)
• Long-Read Pipeline (PacBio & Oxford Nanopore)
• VCF Comparison Pipeline
• Unmapped Reads Statistics
• Logs
• Generation of per structural variation type CSV tables

About

The EFSA Pipeline is designed to process genomic data from multiple sequencing platforms (Illumina, PacBio, and Oxford Nanopore) and perform comprehensive variant analysis including structural variant detection and comparison.