News: Physalia-courses: Eukaryotic-metabarcoding workshop
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3.7 years ago by
carlopecoraro21.8k
Berlin
carlopecoraro21.8k wrote:

Eukaryotic-metabarcoding

Monday 20th to Friday 24th February 2017 in Berlin, Germany http://www.physalia-courses.org/courses/course4/

Instructor: Dr Owen S. Wangensteen (http://www.physalia-courses.org/instructors/t2/)

Overview:

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, 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 community of 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:

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 in a Linux environment. Thus, either a Linux PC or a virtual box running Linux under Windows or Mac environment will be needed. MacOSX systems might be OK, although installation of some additional Python packages might be needed in that case. The syllabus has been planned for people which have some previous experience running simple commands in Linux 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, the main metabarcoding software package we will be using during the course, but no experience with Python is necessary. If in doubt, take a look at the detailed session content below or send Owen S. Wangensteen an email (owenwangensteen@gmail.com).

Where:

Seminar room at Molecular Parasitology, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 14, 10115 Berlin

Course programme:

Session 1. Introduction to metabarcoding procedures. The metabarcoding pipeline.

Session 2. Metabarcoding markers. Primer design. PCR and library preparation protocols.

Session 3. The OBITools pipeline. First steps and quality control.

Session 4. Clustering algorithms. Fixed and variable identity thresholds.

Session 5. Taxonomic assignment. The ecotag algorithm. Reference databases.

Session 6. Generating, improving and curating reference databases.

Session 7. Refining the final dataset. Collapsing, renormalizing and blank correction.

Session 8. Analysing the final dataset. α- and ß- diversity patterns.

Session 9. Presenting the final results. Online resources and future developments.

Session 10. Optional free afternoon to cover previous modules and discuss data.

Further information:

The cost is 430 euros (VAT included) including refreshments and course materials. We also offer an all-inclusive package at 710 euros(VAT included), including breakfast, lunch, dinner, refreshments, accommodation, course and transfer from/to the main city’s airports.

Application deadline is the 20th of January 2017.

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