Analysis of 16S rRNA metagenomic experiments, online

Analysis of 16S rRNA metagenomic experiments, online

omics
Location:

online

Start date:

14 June 2021

Duration:
14 June 2021
15 June 2021
16 June 2021

General context

This training will start with the presentation of a 16S pipeline (psbweb05.psb.ugent.be/lotus/) in a Galaxy environment.

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. If you have no experience with R, you can follow our R introduction 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 :
Raul Tito
VIB - KULeuven

Raul is a PostDoc at the Jeroen Raes Lab of the VIB-KU Leuven Center for Microbiology

Program

10h - 15h How to use Lotus

10h - 16h How to use R to analyze my data

10h - 15h How to use R to analyze my data