Analysis of 16S rRNA metagenomic experiments

Analysis of 16S rRNA metagenomic experiments

Park Inn by Radisson Leuven

Martelarenlaan 36
3010 Leuven
Belgium

04 October 2019

General context

This training will start with the presentation of a 16S pipeline (psbweb05.psb.ugent.be/lotus/) in a linux environment, using a minimal amount of linux commands. This will enable the preprocessing of the data going from raw reads to taxonomic tables and phylogenetic trees.

The 2nd part of the training will give an overview of numerical ecology and takes part entirely in R.

Objectives

Processing and statistical analysis of 16S rRNA metagenomic experiments using R & Lotus pipeline. The following analytical steps from raw data to communicable results will be on the programme:

- Preparation of sequencing data, read filtering, data cleaning

- Data normalization

- Numerical ecology: Clustering, Ordination, Diversity, Modelling

- Univariate & Multivariate Statistics

- Biological interpretation

Required skills

The training is intended for people who have some experience with R and Linux. If you have no experience with R, you can follow our R introduction training first (send an email to bits@vib.be to join this training). If you have no experience with Linux, you can follow our  Linux command line training first. 

Trainers

Falk Hildebrand

Dr. Falk Hildebrand is a bioinformatician with a passion for microbial ecosystems, bacterial evolution and developing computational systems to tackle these subjects in a combined perspective.

He worked during hisPhD at the University of Brussels on bacterial associations to complex diseases such as IBD, obesity and Diabetes. For this, he developed bioinformatic pipelines to process 16S data (LotuS, http://psbweb05.psb.ugent.be/lotus/) as well as the statistical tools.

In his postdoc at EMBL Heidelberg, he continued his research on association to the human microbiome of complex diseases such as Diabetes and Parkinson’s disease. For these projects, he further refined his pipelines, developing the tools necessary to process shotgun metagenomics data and to handle extremely large metagenomic datasets computationally.

He joined the Quadram and Earlham institutes in early 2019, where his group will develop metagenomic tools to track bacterial strains at high resolutions, predict their genomic capabilities and explore their associations to diseases.

Contact Falk Hildebrand :

Program

9h30-12h30: Raw sequence processing

13h30-17h00: Numerical ecology

Practical info

Park Inn by Radisson Leuven

Martelarenlaan 36
3010 Leuven
Belgium

Public transport

Contact

VIB training
Tel: +32 9 244 66 11
Mail: training@vib.be