BIOINFORMATICS II lab microbiome tutorial

Materials below are intended for Jagiellonian University Bioinformatics 2 course. They include all information covered during the lab session.

For more information on Qiita, including Qiita philosophy and documentation, please visit Qiita website.

A description of many of the terms used in this tutorial can be found in this glossary.

This tutorial is adapted from the University of California San Diego Center for Microbiome Innovation (CMI) Qiita/GNPS workshop. You can find more information on the CMI here.

For more comprhensive tutorial on Qiita, please visit the CMI-workshop website. More advanced tutorials in QIIME 2 are available on the QIIME 2 website.

If you have questions about this material, please contact Tomasz Kosciolek.

Qiita tutorials:

Creating a study in Qiita

• Getting example data
  • Processing dataset
  • Analysis dataset
• Setting up Qiita
  • Signing up for a Qiita account
  • Logging into your account and resetting a forgotten password
  • Updating your settings and changing your password
• Studies in Qiita
• Creating an example study
• Adding sample information

Microbiome data processing I

• Adding a preparation template and linking it to raw data
• Exploring the raw data
• Processing 16S data
• The closed-reference workflow
• The deblur workflow
• Running the workflow

Microbiome analyses I

• Analysis of Closed Reference Process
• Rarefying Data
• Taxa Bar Plots
• Alpha Diversity Analysis
  • Observed Operational Taxonomic Units
  • Faith’s Phylogenetic Diversity Index
  • Alpha Diversity Outputs
• Beta Diversity Analysis
  • Bray-Curtis Dissimilarity
  • Unweighted UniFrac Analysis
  • Principal Coordinate Analysis
  • Beta Diversity Group Significance
• Filtering Data
• Filtered Unweighted UniFrac Analysis
• Altering Workflow Analysis Names