Educators:
Sebastian Jünemann (Bielefeld University), Dr. Alex Sczyrba (Bielefeld University), Sebastian Jaenicke (Giessen University), Nils Kleinboelting (Bielefeld University) (BIGI), Johannes Werner (IOW)
Location:
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Room V6-113
Date:
October the 9th to 11th, 2019
Content:
The aim of this 3-day workshop will be to give students a brief overview of the tools and bioinformatics techniques available for the analysis of next generation sequence (NGS) data from microbial communities. The format will comprise a mixture of lectures and hands-on tutorials where students will process example data sets in real-time in the de.NBI cloud environment. After covering general aspects of sequence based analysis (e.g. pre-processing, quality measurements, error handling, and so on) the course is divided into two parts: targeted (16S rRNA gene amplicons) and untargeted (whole-genome shotgun; WGS) metagenome analysis. On demand, a compact introduction into the Linux operating system and the usage of the command line interface will be given upstream to the introducing part to guarantee a consistent baseline for the following lectures. The main aspects of the 16S part are the common pipeline steps beginning with pre-processing and filtering followed by OTU clustering, taxonomic classification, and different statistical measurements. Then, the new ASV/zOTU approach will be introduced followed by similar statistics and both approaches discussed with the attendants in conclusion. In the third part, advantages and disadvantages of whole metagenome sequencing will be illustrated. As WGS metagenomics has the potential to address the full spectra of genome-based issues, the focus here will be on taxonomic and functional analysis with the aid of different bioinformatic tools. Two different techniques to analyze WGS metagenome data are part of this section: (1) in the read-based approach the software solution MGX, an integrated platform for metagenome analysis and data visualization, will be demonstrated. (2) the assembly-based approach to potentially recover near-complete genome by assembling reads into contigs which are subject to binning methods to group individual contigs into genome bins.
Prerequisites:
- basic knowledge in microbiology and NGS-based analysis
- practical experience in a Linux/Unix derivatives, the command line interface and file system required
Prerequisites for the workshop plus the optional Linux introduction:
- basic knowledge in microbiology and NGS-based analysis
Please not that participation to this course does not depend on the actual Linux experience of the applicant. Both, experienced as well as inexperienced Linux users are encouraged to submit an application. However, the Linux introducing session in the morning of the first day is optional only for applicants fulfilling the Linux prerequisite.
Application:
Please send your application to
Website:
For more information see: https://www.cebitec.uni-bielefeld.de/brf/training/upcoming-workshops/110-metagenomics-workshop-10-2019
Contact:
Name: Sebastian Jünemann
Email:
Phone: 0521/106-4827
Name: Dr. Alexander Sczyrba
Email:
Phone: 0521/106-2910
Name: Sebastian Jaenicke
Email:
Phone: 0641/9935-802
Name: Nils Kleinboelting
Email:
Phone: 0521/106-5166