Educators:
Laura Carroll, Nicolai Karcher, Alessio Milanese, Jakob Wirbel, Georg Zeller (HD-HuB)

Date:
18/02/2020 - 19/02/2020
09:00 - 17:00

Location:
ATC Computer Training Lab, European Molecular Biology Laboratory (EMBL)

Contents:
Shotgun metagenomic sequencing approaches are being increasingly employed to characterize the human microbiome. Such complex metagenomics data sets are a rich source for generating functional hypotheses about the roles that gut microbiota play in human health and disease. In this bioinformatics course, participants will be exposed to computational and statistical approaches for the analysis of shotgun metagenomic data. Through a combination of theory-centric lectures and hands-on, practical exercises, the course will cover topics such as taxonomic profiling (i.e., determining “who’s there” in a microbial community), functional analysis (i.e., broadly assessing the functional and metabolic potential of a microbial community, and also mining for specific gene families such as toxins), and comparative metagenomics (i.e., identifying taxa or microbial functions associated with a disease of interest).

Learning goals:
- Pre-processing and quality control of Illumina metagenomic data
- Taxonomic profiling
- Exploratory analyses and visualization methods for metagenomic data
- Functional metagenomic profiling (using both general purpose databases and targeted approaches)
- Comparative analysis of metagenomic data

Prerequisites:
- Familiarity with the Linux command line interface (e.g., running programs from the command line, creating and moving between directories, accessing a remote host via SSH)
- Basic knowledge of the R programming language (e.g., loading data into R, manipulating data frames, creating basic plots)

Keywords:
Metagenomics