3rd de.NBI Training Course on Metagenome Analysis

Educators:
Alex Sczyrba (Bielefeld University), Sebastian Jaenicke (Giessen University), Sebastian Jünemann (Bielefeld University)

Location:
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Room V6-113

Date:
March the 27th to 29th, 2018

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 rDNA operon 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 e.g. OTU clustering, taxonomic classification, and different statistical measurements like rarefaction analysis. In addition, the recent emerging ASV/zOTU approach will be introduced and 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 Linux introduction:
- basic knowledge in microbiology and NGS-based analysis

Please note 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 This email address is being protected from spambots. You need JavaScript enabled to view it. (subject MG­course2018) including a short motivation, a few words about your background, your level of experience on the command line (Linux/Unix), and your experience within the field of metagenomic analysis and related bioinformatic tools. There will be no participation fee, yet travel and accommodation expenses need to be paid by the participants.

Contact:    
Name: Sebastian Jünemann
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: 0521/106-4827

Name: Alexander Sczyrba
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: 0521/106-2910

Name: Sebastian Jaenicke
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: 0641/9935-802

Website:
For more information see: http://www.cebitec.uni-bielefeld.de/polyomics/index.php/training/upcoming-workshops/103-metagenomics-workshop-03-2018