Workshop: eDNA Metbarcoding
When: 19-23 November 2018
Where: Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University, Québec City (Québec), Canada
Dr. Vasco Elbrecht (University of Guelph, Canada)
Eric Normandeau (Laval University, Canada)
Obtaining environmental DNA (eDNA) from water, soil, air, gut content or other sample types holds great promises for biodiversity research and assessment. Targeted species specific markers, and broader, more inclusive metabarcoding approaches using universal primer sets can detect invasive and rare rare species, or the range of taxa present in ecosystems from trace amounts of DNA. eDNA can capture sample diversity using non-invasive or minimally invasive methods/techniques. However, due to the low quantity of DNA present in samples, these approaches often require specialized laboratory protocols, careful sample handling to prevent contamination, as well as specialized bioinformatic processing due to high levels of noise and the presence of non-target taxa.
After completing the workshop, students should be in a position to (1) understand the potential and capabilities of eDNA barcoding and metabarcoding, (2) run complete analyses of eDNA metabarcoding pipelines and obtain diversity inventories and ecologically interpretable data from raw next-generation sequence data and (3) design their own eDNA projects, including bioinformatic data analysis and planning of laboratory work. All course materials (including copies of presentations, practical exercises, data files, and example scripts prepared by the instructing team) will be provided electronically to participants.
While this course will focus on eDNA metabarcoding, however targeted single species detection and other alternatives will also be explored, as they can sometimes be suitable metabarcoding alternatives.
Targeted audience & ASSUMED BACKGROUND
This workshop is mainly aimed at researchers and technical workers with a background in ecology, biodiversity or community biology who want to use molecular tools for biodiversity research, and researchers in other areas of bioinformatics who want to learn ecological applications for biodiversity-assessment. In general, it is suitable for every researcher who wants to join the growing eDNA community. This workshop will review mostly techniques and software useful for eukaryotic single species detection and eDNA metabarcoding. Other workshops focused on procedures currently used in bulk sample and microbial metabarcoding will be available from Physalia-courses. A survey will be provided 2 weeks ahead of the workshop, where participants can mention topics or aspects they are particularity interested in.
No programming or scripting experience is necessary, but some previous expertise using the Linux console and/or R will be most welcome. All examples will be run either in Linux or Mac environments. Please make sure to have linux installed if you bring a Windows based laptop. Among the software and tools we will be using is R or Rstudio (+ the JAMP & PrimerMiner package), FastQC, Usearch, Vsearch, Cutadapt, and mBRAVE.net. No prior knowledge of these software packages is required.
The workshop is delivered over 5 days (see the detailed curriculum below). The lectures are interactive with active discussion where asking questions is strongly encouraged. A key aspect of this course are practical sessions in primer development, bioinformatic analysis of high throughput sequence data, and data visualization as well as a project planning exercise to apply what you learned in this course.
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