Frank Oliver Glöckner, Pelin Yilmaz, Jörg Peplies, Antonio Fernandez-Guerra, Jan Gerken, Ivaylo Kostadinov, Christian Quast, Lorenz Reimer, Anna Vetcininova (BioData)
Maximum Number of Participants:
06-11-2017 to 10-11-2017, 9:00-17:00
Max Planck Institute for Marine Microbiology Bremen
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.
In addition, BacDive - The Bacterial Diversity Metadatabase offers the user a view beyond the primary sequence and its annotation by providing a comprehensive collection of strain-linked information covering the multifarious aspects of bacterial and archaeal biodiversity.
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, design, and evaluation of primers for the amplification of rDNA. 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 gives a 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 sequences/organisms analyzed.
- 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
- 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.
Sequencing technologies, Primers, Contextual data, Standards, Quality assurance, Data submission, Biodiversity statistics, BacDive
- SILVA (http://www.arb-silva.de/) and related/integrated resources
- SILVAngs (https://www.arb-silva.de/ngs/)
- Mothur (https://www.mothur.org/)
- BacDive (https://bacdive.dsmz.de/)