Eukaryotic metabarcoding

Dates

24-28 April 2023

 

To foster international participation, this course will be held online

 

 

Course Overview

Metabarcoding techniques are a set of novel genetic tools for qualitatively and quantitatively assessingbiodiversity of natural communities. Their potential applications include (but are not limited to) accurate water quality, soil diversity assessment, trophic analyses of digestive contents, diagnosis of health status of fisheries, early detection of non-indigenous species, studies of global ecological patterns and biomonitoring of anthropogenic impacts. This workshop gives an overview of metabarcoding procedures with an emphasis on practical problem-solving and hands-on work using analysis pipelines on real datasets. After completing the workshop, students should be in a position to (1) understand the potential and capabilities of metabarcoding, (2) run complete analyses of metabarcoding pipelines and obtain diversity inventories and ecologically interpretable data from raw next-generation sequence data and (3) design their own metabarcoding projects, using bespoke primer sets and custom reference databases. 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.

 

 

Intended audience

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 at 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 communityof metabarcoders worldwide. This workshop will review mostly techniques and software useful for eukaryotic metabarcoding. Another workshop focused on procedures currently used in microbial metabarcoding will be available from Physalia-courses.

 

 

 

Teaching format

The workshop is delivered over ten half-day sessions (see the detailed curriculum below). Each session consists of roughly a one hour lecture followed by two hours of practical exercises, with breaks at the organizer’s discretion.

 

 

Assumed background

The syllabus has been planned for people which have some previous experience running simple commands in Unix and using the R environment (preferently RStudio) for performing basic plots and statistical procedures.

Session content

Monday. 2-8 pm Berlin time

 

Session 1: Introduction to DNA metabarcoding.
In this session participants will be introduced to the key concepts of metabarcoding and we will explain the format of the course. We will outline the different steps of a typical metabarcoding pipeline and introduce some key concepts. Some examples of results that can be obtained from metabarcoding projects are explained. We also talk about technical replication and other experimental design considerations, upscaling methods and biases of metabarcoding. Core concepts introduced: high-throughput sequencing, multiplexing, NGS library, metabarcoding pipeline, metabarcoding marker, clustering algorithms, molecular operational taxonomic unit (MOTU), taxonomic assignment, technical replication, sequencing depth, price per sample, upscaling, methodological biases.

Session 2: Molecular laboratory protocols. DNA extraction. Metabarcoding markers. PCR and library preparation. Good laboratory practice.
In this session we will learn the basics about molecular laboratory procedures needed for metabarcoding. While there will be no hands-on laboratory practices, guidelines and best practices for all key laboratory steps will be discussed. We will explain sample collection techniques, including eDNA and bulk community samples, pretreatment and DNA extraction protocols. The diverse molecular markers available for different kinds of samples and target taxonomic groups will be discussed. Participants will know about sample tags, library tags, adapter sequences, PCR protocols and library preparation procedures. Core concepts introduced: good laboratory practice, proper sample collection, bulk (community DNA) and eDNA samples, DNA preservation, DNA extraction, PCR, clean up, metabarcoding marker, universality, specificity, taxonomic range, taxonomic resolution, primer bias, amplification errors, sequencing errors, DNA contaminations, library generation, sequencing platforms, sample indexing, adapter sequences, index jumping, robotics.

Instructors

 

Prof. Florian Leese

Packages

Package 1

530 €

                                 

 

 

 

                         


Cancellation Policy:

 

> 30  days before the start date = 30% cancellation fee

< 30 days before the start date= No Refund.

 

Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.