From Primer to Paper: Training in Biodiversity Analysis using NGS Amplicon Data

General information

This course falls under the EC H2020 framework of the INMARE project workshop/course on Bioinformatics

Content:
Microbial Diversity analysis, using Next-Generation Sequencing technologies (NGS), have become a routine approach within the last years. Analysis of the ribosomal RNA gene (rDNA) represents the gold standard for microbial identification, phylogeny, and biodiversity studies. Sequencing efforts using this molecule as a marker have been so extensive, that the number of entries for this gene in public repositories has already exceeded 5 million. The understanding of the principles of marker-gene-based sequence analysis using NGS technologies is therefore essential for microbiology, biotechnology, quality control and even clinical diagnostics.

This training course explains all necessary steps researchers need to take when performing amplicon-based investigations using the rDNA as a marker gene. The course starts with experimental design, including an overview of relevant sequencing technologies, and the selection and evaluation of primers for the amplification of the rRNA gene. It teaches the importance of contextual data and standards for data analysis and integration. It provides examples and best practice solutions for data pre-processing and quality assurance up to the contextualized submission of the NGS data to public repositories. It also gives a framework for statistical analysis of the data including a LINUX and R crash course. framework for statistical analysis of the data including a short LINUX and R crash course. Finally, BacDive will be introduced as a tool for further data integration, to better understand the biology of the sequences/organisms analyzed.

Tools (hands-on):
SILVA/SILVAngs, Mothur, BacDive, R, Linux command line

Objective:
  • appropriate experimental design
  • importance of contextual data and standards
  • quality control and quality assurance
  • data submission to public repositories
  • multivariate statistical techniques in microbial ecology
  • concepts and usage of the BacDive metadatabase
Contact Person: Prof. Frank Oliver ( workshops@ribocon.com)

Content

The highlighted icons, represent the fields of education (in compliance with ISCED Classification) engaged during this course/programme.

0512 - Biotechnology", "0688 - Bioinformatics

Venue

Venue: Max Planck Institute (MPI) for Marine Microbiology, Technology Park of the University of Bremen
Bremen, Germany

Celsiusstrasse 1
28359 Bremen
Germany

Application

Open from
1 Aug 2017 to 11 Sep 2017

Cost:

The fee for our Nov 2017 training course is EUR 290 incl. 19% German VAT for each participant.
Foreign participates please note that German VAT must be included in any case because the service is offered within Germany.

Services included are:

  • a four full day training in the topics listed based on lectures, demonstrations, and guided tutorials
  • comprehensive handouts with all lecture slides and other material
  • coffee/tea, soft drinks, and cookies during the course

Travel, accommodation, and full meals are not included.
However, there is a low-priced canteen nearby and we always try to negotiate special rates in selected hotels for our course participants.

The workshop fee has to be paid latest three weeks before the workshop starts.
The invoice including our bank details for payment will be submitted in due time (we also accept credit card payment). As soon as the participation fee has arrived, we will confirm your payment by email.

IMPORTANT: If the workshop fee does not arrive in time on the Ribocon bank account, a confirmation of your administration is required that the fee has already been transferred. In any other case, we will give your place directly to the next one on the waiting list.

Cancellation Policy: All cancellations of registration must be in writing. Compensation fees apply as follows:
50% of the workshop fee for cancellations received 2 weeks before the course starts; complete workshop fee for cancellations received 1 week or less before the course starts.
By registration you agree to these terms.


Prerequisites:
  • the training course is targeted towards biologists that want to apply NGS technologies in their research
  • no programming skills are necessary
  • no prior knowledge about the tools is required

Application Procedure:

Please apply for our Nov 2017 regular training course by sending an email to workshops@ribocon.com with the subject "Training Course Nov 2017" (your email will be confirmed usually within one working day).

Registration mode is Open Application with Selection because of just 11 course places.
Application closes on Sep 11, 18:00 (6 pm) CEST.

Your application mail has to include (i) your full name and (ii) the full address of your institution/company which will also be used as the invoice address later on. Please also include (iii) one short paragraph (max. 200 words) on your background and motivation to join the course.

Your final application status will be communicated latest on Sep 22, 2017. In case of selection your status will change to 'registered' (this then is binding).

Application does not automatically guarantee a place in the course. However, please only apply if you definitely have time to join and also your funding is assured. Thank you!

Qualification

Academic level: Master, PhD, Lifelong Learning
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