The use of amplicons generated by high throughput sequencing methods is now common place, and many avenues exist to learn specific workflows using explicit platforms. There are, however, fewer opportunities to learn the concepts behind amplicon sequence analysis in a platform agnostic way. We are offering an introductory course to amplicon sequence analysis. The course is aimed primarily at newcomers to sequence (amplicon) analysis and will cover the basics from experimental design to basic multivariate analysis of ecological data.

The course will comprise short lectures and hands on exercises. Course notes will be made available. The are no pre-requisites. Students will be expected to install a course virtual machine (supplied prior) to their computers prior to the beginning of the course.

Contact Andrew Bissett for registration and more information.

Contact

Andrew Bissett

Event date: 23Sep 2019

Monday 23 - Friday 27 Sep 2019

CSIRO Hobart

Castray Esplanade, Battery Point TAS
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More information

Instructors:

Course Outline:

Monday Compute set up/introductions
Introduction to jupyter notebook
NGS/multiplexed Amplicon sequencing
Experimental Design
What does sequence data look like and how do I check it out?
•  file formats
Review/questions
Tuesday Initial sequence processing
•  QC and paired end merging
Error correction / denoising
•  When, why, how
Wednesday Clustering
•  When, why, how
Classification
Dealing with large data tables
Python
•  Summary statistics and plots
•  Review and Questions
Thursday Data curation - trying our best to avoid catastrophic mistakes
Alpha diversity
•  Coverage
•  Diversity indices
•  Rarefaction
•  Linear models - fitting, diagnostics, predictions, multiple comparisons
Ordination
•  Choice of approach (PCA/CA/PCoA/NMDS)
•  Data standardisation (binary/counts/relabund/Hellinger/CoDa)
•  Interpreting output (loadings, associations)
•  Plotting
Friday Constrained ordination
•  Choice of approach (RDA/CCA/CAP)
•  Data standardisation (scaling/transformation/categorical)
•  Choosing predictors (vif/envfit/ordistep)
•  Interpreting output
• Plotting
Variation partitioning
•  Estimates and hypothesis tests
•  Spatial predictors
Experimental frameworks
•  PerMANOVA
•  Dispersion
•  Plotting

Science areas:

Event type: Exhibition or workshop