Getting Ready for the Workshop

Please complete the following four steps to prepare the workshop:

1. Install software and redeem your voucher
2. VM Setup Instructions
3. Start Jupyter
4. Pause Your VM

Resources

Here is a list of resources relevant to this workshop.

Materials From This Workshop

• Metagenomics Overview Slides
• GitHub Repository
• Docker Image

Microbiome Resources

• Dada
  • DADA2 preprint
  • Dada2 Github Repository
• Phyloseq
  • Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
  • phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
• Qiime
• Mothur
• Earth Microbiome Project Protocols

General Computational Resources

• Azure
  • Azure in education
  • Azure for Research
• Docker
  • Docker Machine
• Jupyter
  • Jupyter Docker Stacks
• RStudio

Reproducible Research

• SRA
• Ten Simple Rules for Reproducible Computational Research
• Reproducible research, training wheels, and knitr