26 February-2 March 2018
Metabarcoding techniques are a set of novel genetic tools for qualitatively and quantitatively assessing biodiversity 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, 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.
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 community of metabarcoders worldwide. This workshop will review mostly techniques and software useful for eukaryotic metabarcoding. Other workshops focused on procedures currently used in microbial metabarcoding will be available from Physalia-courses.
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.
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, with some ssh connections to remote servers. For Windows users, a virtual box running Linux under Windows and/or the installation of an ssh client (e.g. PuTTY) will be needed. For MacOSX systems, installation of some additional Python packages might be needed for running the OBITools software suite. The syllabus has been planned for people which have some previous experience running simple commands from a terminal in Linux or Mac and using the R environment (preferently RStudio) for performing basic plots and statistical procedures. You will need to have a laptop with Python 2.7 installed for running OBITools, but no experience with Python is necessary. If in doubt, take a look at the detailed session content below or send to us.
Monday 26th – Classes from 09:30 to 17:30
Session 1. 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. Some examples of results that can be obtained from metabarcoding projects are explained. We will outline the different steps of a typical metabarcoding pipeline and introduce some key concepts. We 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: high-throughput sequencing, multiplexing, NGS library, metabarcoding pipeline, metabarcoding marker, clustering algorithms, molecular operational taxonomic unit (MOTU), taxonomic assignment.
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