Comparative metagenome analysis with MGnifyR – Practical
Comparative metagenome analysis – Practical
Trainer: Jennifer Lu, and Alejandra Escobar-Zepeda
Metagenomics is the study of genetic material(s) recovered directly from environmental samples. The analysis of metagenomic datasets from high-throughput sequencing is aimed at determining the biological diversity (e.g. taxonomic composition, functional potential etc) of microbial communities of interest as an ecological entity. Comparative metagenomics provides a powerful tool set for highlighting the differences between groups of samples, and is now commonly used to analyse samples across different timepoints, states of health, and geographical locations etc. The theoretical session will cover some key methods for comparative metagenomic analysis, while the practical session will allow users to make use of an actual analytical pipeline using publicly-available data from MGnify. We will review methods for whole community comparisons and tools that discern taxon-specific group associations in a differential abundance analysis.
Learning outcomes
After this session you should be able to:
- Fetch and process metagenomics analysis results from MGnify website using MGnify R tool
- Test different normalization methods and run a comparative metagenomics analysis at microbial community level
- Compute a differentially abundant taxa test and generate a predictive model using machine learning
Materials