• Event
  • Scientific training

Microbial Community Analysis Workshop 2022

Microbiome analysis going from samples, to sequencing, to numerical ecology analysis

Start date:

29 March 2022

End date:

31 March 2022

Time:

10h00 - 16h00

Venue:

Virtual (via Zoom)

Enquiries:

training@earlham.ac.uk

Registration deadline:

27 February 2022

Cost:

£50

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.

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.

Programme.

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

Time

Topic

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

Break

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

Time

Topic

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

Break

13:15 - 14:45

Removing contaminants, quality control (continued)

14:45 - 16:00

Data normalization, alpha diversity

Day 3 - 31 March 2022

Time

Topic

10:00 - 12:00

Differential taxa abundances

12:00 - 13:00

Break

13:00 - 15:00

Beta diversity, Ordination, Neutrality

15:00 - 15:30

Wrap up and Close

Further information.

Please carefully review our standard online event booking terms and conditions prior to registering for this event. Completing an online registration and associated payment process will mean that you are bound by these terms and conditions. Any supplemental terms or changes to these conditions on a per event basis will be included on this page. If you have any queries regarding our events or in relation to your booking, please contact us at training@earlham.ac.uk

  • Register today.

Registration deadline: 27 Feb 2022 - 23:45

Participation: First come, first served