2021-edition

The international MDAW workshop brings together leading data scientists to discuss their newest developments, statistical tools, and latest findings in the rapidly expanding field of microbiome data analyses and high-throughput sequencing. MDAW is held to encourage PhD students and Postdocs dealing with large and complicated, highly dimensional microbiome datasets, to get an overview of the current state-of-the art in amplicon sequence data analyses, teached in lectures and hands-on sessions. Of course this workshop also aims to promote scientific networking and international research collaborations!

On behalf of the organizing committee,
Professor Dr. Olivier Thas (Data Sciences Institute, UHasselt),
dr. Sofie Thijs (Center for Environmental Sciences, UHasselt)

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Target audience: All Scientists, Biology, Biomedical Sciences, Biostatistics, Bioinformatics

Skills level: Beginner to advanced.
Hands-on sessions are targeted for beginners in R, Linux, python.

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General context (2021 edition)

The following topics are covered in this workshop:

• We execute a workflow to go from raw fastq files to an OTU-table
• We use the generated OTU-table for basic data visualisation, data exploration and differential abundance analyses
• We will identify biomarkers in high-dimensionality microbiome datasets
• We perform a multidata visualisation using Circos
• We use the tool manta and anuran to perform a microbial community network analyses
• We perform a metagenome-wide-association analyes (MWAS) on a microbiome dataset
• We execute the PEMA pipeline to process 16S, ITS, 18S and COI amplicon data, and visualisation in phyloseq
   

Objectives
In this workshop participants will get a better understanding of how to analyse their amplicon microbiome sequencing data starting from the raw reads (.fastq) to ASV/OTU-table, and a better notion on the downstream biostatistical analyses and associated challenges. Topics that will be critically discussed include: data visualisation, diversity estimation, normalisation prior to differential abundance testing, biomarker discovery, latent variable models of the microbiome, multi-data integration, and ecological network analyses, modelling, stability and multistability, to phylogeny-aware methods in beta-diversity microbiome analyses, concluding with eco-evolutionary modelling and metagenome-wide-association (MWAS) studies. The 4th day will address besides bacterial 16S rRNA gene amplicons, also eukaryotic 18S rRNA, ITS and COI marker gene amplicon datasets. The raw reads will be processed using the pipeline PEMA (Pipeline for Environmental DNA Metabarcoding Analysis), followed by downstream R analyses.

The topics will be introduced in lectures, and virtual hands-on sessions. 

Required skills
Basic familiarity with the Illumina sequencing process and FastQ format. Also basic familiarity with R and the package phyloseq. Basic notion of Linux.

Softwares and R packages demonstrated:
DADA2
phyloseq and packages
ggplot2, tidyverse, ggpubr
Rmarkdown
Deseq2
Cytoscape
Circos
manta
anuran
PEMA
....