Educators:
Alexander Sczyrba, Sebastian Jünemann, Nils Kleinbölting (BiGi), Franziska Klincke (University of Copenhagen), Joseph Nesme (University of Copenhagen),

Location:
Online

Date:
February 2nd to 5th, 2021

Content:
The aim of this 4-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: whole-genome shotgun (WGS) metagenome analysis and ecological statistics. If necessary, a compact introduction into the Linux operating system and the usage of the command line interface will be given on the first day to guarantee a consistent baseline for the following lectures. On the first day of the metagenomics course, 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 assembly, binning and taxonomic and functional analysis with the aid of different bioinformatic tools. The aim of the second part of the course is to give students a basic understanding of ecological statistics and apply it to census data typically obtained from shotgun metagenome analysis. Using R and the RStudio environment, the workshop will consist in a short introduction of the R programming language and hands-on method to import count data, store it in the PhyloSeq class object and use this object to: 1) calculate within (alpha-) and between (beta-) diversity of samples groups; 2) perform differential abundance testing between case and control; 3) produce and display correlations. The workshop will use a real study metagenomic sequencing dataset and help the students to produce quality figures for all aspect covered in the course with reproducible R scripts.

Prerequisites:
- basic knowledge in microbiology and NGS-based analysis
- practical experience in a Linux/Unix derivatives, the command line interface and file system required

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.