Comparative metagenome analysis – Lecture
Trainer: Jennifer Lu, and Alejandra Escobar-Zepeda
Overview:
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:
- Identify the that diversity is used to look at the variability in microbiome data. Alpha: intra-sample variability ♦ Beta: inter-sample variability
- Identify the used metrics in comparative genomics and be aware that the used metrics depend on the data and the question posed
- Identify the differential abundant taxa used to explore difference in taxa between different populations
Materials: