How-To Guides

Practical guides for common tasks and specific use cases with the Sanger DNA Damage Analysis Pipeline.

🎯 Overview

These guides provide step-by-step instructions for specific tasks and workflows. Each guide focuses on solving a particular problem or achieving a specific goal.

Analysis Workflows

📚 Guide Categories

Data Preparation 🗂️

Getting your data ready for analysis, organizing files, and initial quality checks

Analysis Workflows ⚙️

Different approaches to running analyses based on your research needs

Ancient DNA Specific 🧬

Specialized workflows for ancient DNA research and authentication

Customization 🔧

Adapting the pipeline for specific research requirements

Reporting and Visualization 📊

Creating reports, exporting data, and generating visualizations

Troubleshooting 🔍

Solving common problems and optimizing performance

🚀 Quick Access

Most Popular Guides:

  • Process Single Sample - Process a single sample from start to finish

  • batch_processing - Efficiently process multiple samples

  • assess_damage_patterns - Evaluate ancient DNA damage

  • create_custom_config - Customize pipeline settings

  • debug_failed_runs - Troubleshoot analysis problems

By Research Type:

  • Ancient DNA Researchers: Start with assess_damage_patterns and handle_degraded_samples

  • Modern DNA Analysis: See Process Single Sample and quality_assessment

  • High-Throughput Labs: Check out batch_processing and performance_optimization

  • Method Development: Look at modify_hvs_regions and integrate_external_tools

💡 How to Use These Guides

Each guide includes:

  • Goal: What you’ll accomplish

  • Prerequisites: What you need before starting

  • Step-by-step instructions: Detailed commands and explanations

  • Expected outputs: What results to expect

  • Troubleshooting: Common issues and solutions

  • Next steps: Related guides and advanced topics

Reading Level: * 🟢 Beginner: Basic pipeline usage * 🟡 Intermediate: Some experience with bioinformatics * 🔴 Advanced: Experienced users and developers

🔗 Prerequisites

Before following these guides:

  • ✅ Pipeline installed and working (see Installation)

  • ✅ Basic command line familiarity

  • ✅ Understanding of FASTA format and sequence data

  • ✅ Access to AB1 sequencing files

📋 Guide Index by Task

File Management: * prepare_ab1_files - Prepare and validate AB1 input files * organize_samples - Structure your data for efficient processing * export_data - Export results in various formats

Quality Control: * quality_assessment - Assess sequence quality before processing * handle_low_quality_data - Work with poor-quality samples * debug_failed_runs - Diagnose and fix processing failures

Analysis Types: * Process Single Sample - Single sample workflow * batch_processing - Multiple sample processing * comparative_analysis - Compare results across samples

Ancient DNA: * assess_damage_patterns - Identify and quantify damage * validate_authenticity - Statistical validation of ancient DNA * handle_degraded_samples - Optimize for degraded samples

Configuration: * create_custom_config - Create project-specific configurations * modify_hvs_regions - Customize HVS region definitions * integrate_external_tools - Add new analysis tools

Visualization: * generate_publication_reports - Create publication-ready reports * create_custom_plots - Generate custom visualizations

Performance: * performance_optimization - Speed up processing * batch_processing - Efficient multi-sample workflows

🆘 Getting Help

If you can’t find what you’re looking for:

  1. Search the documentation using the search box

  2. Check related guides at the bottom of each guide

  3. Review the troubleshooting guides for common issues

  4. Open an issue on GitHub with specific questions

  5. Join the community discussions for help and ideas

💬 Contributing Guides

Help improve these guides by:

  • Reporting issues: Found an error or unclear instruction?

  • Suggesting improvements: Have ideas for better explanations?

  • Contributing new guides: Want to share a useful workflow?

  • Providing feedback: Let us know what’s helpful or confusing

Let’s solve your specific analysis challenges with these practical, step-by-step guides!