Workshop 5 Introduction Slides

Authenticating Ancient DNA and Quality Control

• Ancient DNA is often degraded and contaminated
• Authenticity and quality must be assessed before downstream analysis
• Use LLMs to help generate, debug, and interpret QC code

Problem Statement

• Implement QC checks (read length distribution, GC content, damage patterns)
• Authenticate ancient DNA using computational methods
• Interpret QC outputs and summarize findings for your PI

Why Quality Control for Ancient DNA?

• Ensures data is authentic and suitable for analysis
• Detects contamination, degradation, and other issues
• Guides decisions on whether to proceed or re-sequence

Workshop Workflow: Problem → Prompt → Code → Debug → Result

• Problem: Define the QC and authentication challenge
• Prompt: Craft an effective LLM prompt
• Code: Generate and run QC scripts and rules
• Debug: Identify and fix QC issues
• Result: Summarize and interpret QC findings

Getting Started: Example LLM Prompt

I need to perform quality control on ancient DNA FASTQ/FASTA files, including read length distribution, GC content, and damage pattern analysis. Please generate Python or bash scripts and Snakemake rules to automate these QC checks and summarize the results.