Repository for workshop Microbiome analysis using 16S rRNA gene libraries workshop

Developed for University of British Columbia MICB 506 class

By Erick Cardenas Poire and Michael Murphy

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This repository contains:

• The powerpoint presentations:

  • Introduction to diversity analysis (File 1).
  • Use of 16S rRNA as phylogenetic marker in diversity studies (File 2).
  • Mothur tutorial using the Miseq SOP (File 3).

• The Miseq tutorial is based on the mothur Miseq:

  • We will run a modified version of the Miseq tutorial. The guide is here.
    The main difference is that we will not run a phylotype analysis and use fewer samples to make it run faster.
    The original Miseq SOP is available here_.
  • You need a computer with Mothur installed. Installers are available here_.
  • The Silva-based bacterial reference alignment is here.
  • Mothur-formatted version of the RDP training set v.9 is here_.
  • The data files required are here.

• Other resources:

  • Tree diversity analysis book by Roeland Kindt and Richard Coe.
    A nice introduction to diversity analysis. Is also includes detailed R code.
    Freely available here.
  • Multivariate analyses in microbial ecology by Alban Ramette. A minireview freely available here.
  • If you are going to be working with 454 data (pyrosequencing), mothur also has a protocol for in here_.