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
-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.