Please Note: This event is now fully booked. Please contact training@earlham.ac.uk to be notified of future dates.
Microbiome analysis going from samples, to sequencing, to numerical ecology analysis.
This three-day course will provide an overview of metagenomics analysis, going from raw sequencing reads to publication ready analysis and Figures.
On day 1, we will cover the theory of DNA extraction, sample storage and discuss existing pipelines for amplicon sequencing. We will introduce and use the LotuS2 pipeline on an example dataset, relying on its Galaxy interface that is usable in a web browser.
Day 2 and 3 of the course will focus on exploration of the abundance data from producing diversity measures to visualisation of taxonomic differences, using R. This part is also applicable to shotgun metagenomics experiments.
What will I learn?
- Metagenomic experiment planning, execution and analysis
- Analysing amplicon sequencing data with up-to-date tools and how to increase the quality of ASVs and OTUs, when to use what technique
- Postclustering 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
Who is this training for?
Early career scientists and bioinformaticians undertaking a research project involving metagenomic analysis and wanting to produce OTU and taxa abundance tables using a streamlined & speedy pipeline.
Prerequisites:
As the majority of the course will be held in R, having some basic R experience is important, including being able to use functions such as “read.table”, “plot”, and knowing what a variable is and how to save them. If you can complete the Carpentries lesson here, then you will be prepared to follow the training course.
This training forms part of our BBSRC National Capability in Advanced Training
The workshop is being led by Dr Falk Hildebrand, joint Group Leader at Quadram Institute and Earlham Institute.
