- Scientific training
Microbial Community Analysis Workshop 2022
Microbiome analysis going from samples, to sequencing, to numerical ecology analysis
29 March 2022
31 March 2022
10h00 - 16h00
Virtual (via Zoom)
27 February 2022
About the event.
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.
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.
Organisers and trainers.
Day 1: Amplicon sequencing pipelines and LotuS2 hands-on
Day 2: Using R to analyse and prepare 16S data
Day 3: Numerical ecology in R
Please note that breaks (including lunches) will be taken dynamically and won’t necessarily be at set times
Day 1 - 29 March 2022
10:00 - 11:30
Welcome and Flash talks
11:30 - 12:30
Experimental Design, DNA extraction, 16S amplification (functional genes amplicon sequencing), qPCR
12:30 - 13:15
13:15 - 14:00
Existing pipelines analysis of amplicon sequencing data
14:00 - 14:45
Filtering, removing chimeric sequences and clustering high quality OTUs
14:45 - 15:30
Introduction to Galaxy
15:30 - 16:00
Preparing data for LotuS2 - creating a map file/uploading data to your Galaxy account / first LotuS run
Day 2 - 30 March 2022
10:00 - 11:30
Hands on: Basic demultiplexing and filtering, tax assignments, phylogenies, offtargetDB, chimeras, clustering algorithms, sdm options, mapping file
11:30 - 12:30
Removing contaminants, quality control
12:30 - 13:15
13:15 - 14:45
Removing contaminants, quality control (continued)
14:45 - 16:00
Data normalization, alpha diversity
Day 3 - 31 March 2022
10:00 - 12:00
Differential taxa abundances
12:00 - 13:00
13:00 - 15:00
Beta diversity, Ordination, Neutrality
15:00 - 15:30
Wrap up and Close
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Registration deadline: 27 Feb 2022 - 23:45
Participation: First come, first served