This training will start with the presentation of a 16S pipeline in a Galaxy environment. This will enable the preprocessing of the data going from raw reads to taxonomic tables and phylogenetic trees.
The 2nd part of the training will give an overview of numerical ecology and takes part entirely in R (meaning that knowledge of R is mandatory).

Objectives

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 program:

• Metagenomic experiment planning, execution and analysis
• Analyzing amplicon sequencing data with up-to-date tools and how to increase the quality of ASVs and OTUs, when to use what technique
• Post-clustering of ASVs to avoid intra-genomic ASV false-positives
• Working with low-biomass experiments, removing exogenous contamination in several scenarios
• Numerical ecology focused analysis workflow for both metagenomic and amplicon sequencing based studies
• Analysis of alpha/beta diversity
• Univariate statistics to identify species enriched in sample groups
• Multivariate statistics and visualization to identify clusters of samples
• Assessing microbial communities based on ecological principles and species distributions

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