This training will start with the presentation of a 16S pipeline in a linux environment, using a minimal amount of linux commands. This will enable the preprocessing of the data going from raw reads to taxonomic tables and phylogenetic trees. The second part of the training will give an overview of numerical ecology and takes part entirely in R.

Objectives

The main objective is to demonstrate the processing and statistical analysis of 16S rRNA metagenomic experiments using R & Lotus pipeline. The following analytical steps from raw data to communicable results will be on the programme:

• Preparation of sequencing data, read filtering, data cleaning
• Data normalization
• Numerical ecology: Clustering, Ordination, Diversity, Modeling
• Univariate & Multivariate Statistics
• Biological interpretation