June 27-29, 2011

Module 14: Introduction to Metagenomic Data Analysis

Instructors: Alexander V. Alekseyenko and Susan P. Holmes

Module description: This course is concerned with analysis of microbial community data generated by next-generation sequencing technologies. These high-throughput methods allow for deep surveying of microorganisms inhabiting their biological hosts. We will cover the steps for preprocessing Roche 454 sequencing data and the Phylochip data, necessary to produce abundance tables. We will then examine methodology for associating microbial abundance data with experimental factors and outcomes. Programming will be done in R, and overview of available programs for preprocessing the data will be provided.

Module 14 : Agenda

Lecture 1: Introduction: Biological questions addressed by metgenomic analysis
Lecture 2: Technologies for metagenomic data
Next Generation Sequencing
Lecture 3: Phylochip Microarray Data
Lecture 4: Amplicon data analysis pipelines: Introduction to QIIME
Lecture 5: VirtualBox Installation

VirtualBox Machine
Lecture 6: QIIME tutorial
Lecture 7: Introduction to Multivariate Data Analysis
Lecture 8: Phylochip Data and Trees
Lecture 9: Testing and Multiple Testing
Lecture 10: Multivariate Methods for Abundance and Presence/Absence
Lecture 11: Combining Trees and Other Data
Lecture 12: Multiple Table Methods
Lecture 13: Networks (a: Alex). Networks (b: Susan).
References: File Here
Data: Data Sets
Labs: Labs

  © 2011 Susan Holmes