CUrriculum

Monday - 9:30 - 17:30

 

 

-Introductions and course overview

 

-Environmental DNA research and experimental design

 

-PRACTICAL:Getting started with UNIX

 

 

 

 

Tuesday - 9:30 - 17:30

 

 

-Single species detection using qPCR

 

-qPCR primer selection and primer design

 

PRACTICAL: in silico qPCR primer design and selection

 

 

 

 

Wednesday  -  9:30 - 17:30

 

 

-Introducing eDNA metabarcoding, monitoring biological communities using high throughput sequencing (HTS).

 

-Metabarcoding primer selection, overview of different primers and targets.

 

-Overview of the lab work to construct Illumina libraries, concepts in sequencing.

 

PRACTICAL: Getting started with R, HTS data input and quality control.

 

 

 

 

Thursday -  9:30 - 17:30

 

 

-Bioinformatic pipelines, operational taxonomic units (OTUs) clustering vs denoising

 

-Taxonomic assignment, sequence databases

 

PRACTICAL: Sequences to tables, clustering and denoising eDNA data to make biologically meaningful groups.

 

 

 

 

Friday -  9:30 - 17:30

 

 

-Ecological analyses

 

-Ordination methods for eDNA metabarcoding data

 

-Linear and generalized linear models introduction

 

PRACTICAL: Preliminary statistical analysis of qPCR data and OTU tables using ordination and lm/glm in R, Generating plots in R.

 

 

 

Final afternoon session (3:30 onwards) participant project discussion and travel time for those who need to leave.