Tutorials

Step-by-step tutorials for common workflows with the Sanger DNA Damage Analysis Pipeline.

🎯 Tutorial Overview

These tutorials walk you through real-world scenarios and best practices for using the pipeline effectively.

Basic Tutorials

• Your First Analysis
  • 🎯 Tutorial Goals
  • 📋 Prerequisites
  • 💾 Sample Data Setup
  • 🚀 Step 1: Configuration Setup
  • 🔧 Step 2: Run the Complete Pipeline
  • 🗂️ Step 3: Explore the Output Structure
  • 📊 Step 4: Generate Interactive QC Report
  • 🔍 Step 5: Interpret Your Results
  • 📈 Step 6: Examine Individual Results
  • 🎯 Step 7: Understanding Your Results
  • 🔧 Step 8: Check Pipeline Status
  • 🚨 Troubleshooting Common Issues
  • 🎉 Congratulations!
  • 🎯 Next Steps
  • 🔄 Practice Exercises
  • 💡 Key Takeaways

📚 Tutorial Levels

Beginner 🟢

Basic pipeline usage, standard configurations, simple analyses

Intermediate 🟡

Custom configurations, ancient DNA analysis, quality optimization

Advanced 🔴

Batch processing, automation, custom analysis workflows

🚀 Getting Started

If you’re new to the pipeline, start with:

1. Your First Analysis - Your first complete analysis

2. basic_workflow - Understanding the standard workflow

3. quality_control - Interpreting quality metrics

For ancient DNA researchers:

1. ancient_dna_workflow - Specialized ancient DNA workflow

2. damage_assessment - Understanding damage patterns

3. statistical_validation - Bootstrap analysis and significance

For advanced users:

1. batch_processing - Processing multiple samples efficiently

2. automation - Setting up automated workflows

3. custom_configurations - Creating specialized configurations

💡 Tutorial Features

Each tutorial includes:

• Step-by-step instructions with command examples

• Expected outputs and how to interpret them

• Troubleshooting tips for common issues

• Best practices and recommendations

• Real data examples when possible

🔗 Prerequisites

Before starting the tutorials, ensure you have:

• ✅ Pipeline installed (see Installation)

• ✅ Dependencies configured (MAFFT, Python packages)

• ✅ Basic understanding of command line usage

• ✅ Sample AB1 files to work with

🆘 Getting Help

If you get stuck during any tutorial:

• Check the troubleshooting section in each tutorial

• Refer to the main Troubleshooting guide

• Open an issue on GitHub with your specific problem

• Include error messages and configuration details

Let’s get started with your first analysis!