Eukaryotic-metabarcoding

Dates

22 – 26 February 2021

Due to the COVID-19 outbreak, 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 examplescripts 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 inLinux and using the R environment (preferently RStudio) for performing basic plots and statistical procedures.

Session content

Monday. 2-8 pm Berlin time

 

Session1. Introduction to metabarcoding procedures. The metabarcoding pipeline. In this session students will be introduced to the key concepts of metabarcoding and the different next-generation sequencing platforms currently available for implementing this technology. The kind of results that we may obtain from metabarcoding projects is explained using examples from real life. I will outline the different steps of a typical metabarcoding pipeline and introduce some key concepts. I will also explain the format of the course. In this session, we will check that the computing infrastructure for the rest of the course is in place and all the needed software is installed. Core concepts introduced: next-generation sequencer, multiplexing, NGS library, metabarcoding pipeline, metabarcoding marker, clustering algorithms, molecular operational taxonomic unit (MOTU), taxonomic assignment.

Instructors

Packages

                                 

 

 

 

                         


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.