Joint de.NBI & DZIF Training Course on Targeted and Untargeted Metagenome Analysis

Educators:
Dr. Alex Sczyrba (Bielefeld University, DE) (BiGi / de.NBI)
Dr. Christopher Quince (Glasgow University, UK)
Dr. A. Murat Eren (University of Chicago, USA)
Andreas Bremges (DZIF)
Sebastian Jünemann (BiGi / de.NBI)

Date:
August 29th to September 2nd, 2016

Location:
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Room V0-133

Content: The aim of this 5-day workshop will be to give students an overview of the tools and bioinformatics techniques available for the analysis of next generation sequence 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. After covering general aspects of sequence based analysis (e.g. data pre-processing, quality measurements, data filtering, and so on) the course is divided into two parts: untargeted (whole-genome shotgun; WGS) targeted (16S rDNA operon gene amplicons) and metagenome analysis. The main aspects of the 16S part are the common pipeline steps beginning with pre-processing, OTU clustering, taxonomic classification, normalization, and different statistical measurements like rarefaction analysis. Problems and pitfalls as well as the correct usage of different specialized data bases will be discussed with the attendants in conclusion. In the WGS 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, with a special focus on binning methods to potentially recover near-complete genomes from metagenomes. Students will also be encouraged to bring their own data for analysis.

Prerequisites:
- Basic knowledge in microbiology and NGS-based analysis
- Experience with a Linux command line recommended but not required

Tools:
Qiime, MGX, MetaBat, MegaHit

Keywords:
Metagenomics, 16S, WGS, Assembly, Amplicon,

Contact:
Name: Andreas Bremges
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: 0521/106-2914

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

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

Website:
For more information click here