Microbiome Course

Course Outline

• Work through DNAnexus?
• Find a nice cancer data set for 16S and shotgun
• Divide into two workshops or courses?
• Course structure or workshop structure?

Amplicon processing and analysis (5 week course)

(4 weeks) 1. Talk by Greg Caparaso? 1. What is the microbiome? 1. Experimental design considerations
2. Why use qiime2? 3. Primary features, new developments specifically relevant to cancer researchers 2. Importing, Demultiplexing, sample metadata 3. Trimming, potentially read joining (needed for deblur), OTU clustering, denoising 5. Taxonomic classification, phylogeny 6. Alpha diversity 7. Beta diversity 8. Other analyses 1. longitudinal 2. random forests 3. differential abundance 9. Exporting to R: qiime2R

Shotgun Analysis / functional profiling 1. What can we do with qiime2? 1. Taxonomic 1. q2-shogun 2. q2-metaphlan2 2. What is biobakery? (focus on workflows) 1. HUMAnN3 workflow - functional profiling 2. metaphlan2 - taxonomic profiling 3. strain profiling 3. Genome assembly route 1. https://genomics.sschmeier.com/ngs-assembly/index.html# 4. Other resources 1. Nephele 1. Get someone from NIAID to talk about what can be done with this resource? 1. https://bioinformatics.niaid.nih.gov/resources#35.1.1 2. https://nephele.niaid.nih.gov/user_guide/ 2. Calypso 3. Kbase 4. Clc genomics - microbiome 1. https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-clc-microbial-genomics-module/ (proprietary) 5. https://metagenomics.sequentiabiotech.com/TaskResource (proprietary) 6. PATRIC

Can have additional R specific courses at a later date: phyloseq, microbiomeseq, etc.

Emily Vogtmann ---- published papers