Educators:
Sebastian Jünemann, Nils Kleinboelting, Alexander Sczyrba (BiGi) Liren Huang, Kassian Kobert, Zhi-Luo Deng (NFDI4Microbiota)

Date:
November the 7th to 9th, 2023

Location:
Bielefeld University

Contents:
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. 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. After covering general aspects of sequence based analysis (e.g. pre-processing, quality measurements, error handling) advantages and disadvantages of whole metagenome sequencing will be illustrated. As WGS metagenomics has the potential to address the full spectrum of genome-based issues, the focus here will be on assembly, binning and taxonomic and functional analysis with the aid of different bioinformatic tools. In the last part, nextflow workflows will be introduced to make use of nf-core workflows for automated and reproducible metagenomic analysis.

Prerequisites:
This is a course for beginners. There are no prerequisites for the participants except some basic knowledge in microbiology, NGS data and NGS-based analysis.