Joint NFDI, de.NBI & DZIF Metagenomic Training Course 2024

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. 

Agenda:

Tue, Feb 6, 2024, 11 am - 5 pm:
Introduction to de.NBI, NFDI4Microbiota & de.NBI Cloud, Introduction to Linux, Data Processing

Wed, Feb 7, 2024, 9 am - 5 pm:
Metagenomics - Introduction & Assembly, Assembly Evaluation, Binning, MAG Classification & Annotation
Data Processing - ENA Data Submission

Thu, Feb 8, 2024, 9 am - 4 pm:
Nextflow Workflows - Introduction into Nextflow, nf-core for Assembly, Binning & Profiling, Hands-on nf-core

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. 

Application:
The course is already fully booked. Registration is ufortunately no longer possible.

Contact:
If you have any questions regarding the workshop, please do not hesitate to email us at s.juenemann@fz-juelich.de (related to topics of the course) or cordula.hege@helmholtz-hzi.de (organisational things).