Test 2 Description

I have taken the Saccharomyces cerevisiae genome and engineered in 5000 SNPs. Then I simulated 4 sets of Illumina reads from that genome. They vary in quality, level of adapter or poly-G contamination, and coverage. Your job is to

• Use the pipeline from class labs to call SNPs from the original Saccharomyces cerevisiae genome (which I will provide). Your job is to find those 5000 snps.
• Along the way you will find the quality issues in each sample and compare how those quality issues do or do not impact downstream snp calling.
• Document your work on a github wiki, send in multiqc reports from each step, and answer some questions about your analysis.
• Finally, compare the class pipeline to the pipeline from your AI SNP calling exercise that you turned in as homework. I will be providing some specific questions to think about and answer.

I'm still working on github wiki template to help guide your work. To get set up:

• Register a github account if you don't already have one
• Create a new repository called "EPP622-2026-SNPCalling"
• Go to the wiki tab at the top and start your documentation there.
• Github wikis use the markdown language for formatting, learn more here