Workshop 4 Introduction Slides

Comparative Analysis of Multiple Ancient Samples

• Extend your workflow to analyze and compare multiple ancient mitochondrial genomes
• Automate batch downloads, run analyses, and generate comparative plots
• Use Snakemake and LLMs to streamline the process

Problem Statement

• Download multiple ancient mitochondrial genome FASTA files from a public database
• Compute sequence statistics for each sample
• Generate comparative plots (e.g., GC content distribution)
• Summarize your approach and findings for your PI

Why Compare Multiple Samples?

• Reveals biological variation and patterns across individuals
• Enables population-level insights
• Demonstrates the power of automation and reproducible workflows

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

• Problem: Define the comparative analysis challenge
• Prompt: Craft an effective LLM prompt
• Code: Generate and run batch processing rules
• Debug: Identify and fix errors in batch workflows
• Result: Summarize and interpret comparative findings

Getting Started: Example LLM Prompt

I need to download and analyze multiple ancient mitochondrial
genome FASTA files from a public database. Please generate
Snakemake rules and Python code to batch process each sample,
compute sequence statistics, and generate a comparative GC
content plot.