Lab course: NGS Technologies,
Plant Omics and Data Analysis

11-20 October 2023 at the Higher Institute of Biotechnology of Sfax

This lab course aims to up-skill the Tunisian community in the use of NGS technologies and bioinformatics tools for the analysis of plant omics data. Focus has been made on genomic, transcriptomic and metabolomic data. 

Trainers

Manuel Spannagl (HMGU, Germany)

Nadia Kamal (HMGU, Germany)

Klaus MAYER (HMGU, Germany)

Anca Macovei (University of Pavia, Italy)

Andrea Pagano (University of Pavia, Italy)

Daniele Dondi (University of Pavia, Italy)

Dhana Vadivel (University of Pavia, Italy)

Main topics

 

-Introduction to Bioinformatics: how can bioinformatics support my lab results etc

– Databases: how and where to find public data

– Hands-on: Finding all needed data (genome, gff and annotations, RNAseq data)

– Introduction to NGS and transcriptomics (techniques, design NGS experiments, fasta vs fastq, available tools, QC and trimming, explanation of example data)

– Hands-on: Processing raw data (fastp and/or Trimmomatic/FastQC → MultiQC, RseQC)

– Mapping, DGE and annotation (genome and transcriptome mapping, PCA)

– What analysis can be done with the data?

– How to annotate genes (Mercator, Interproscan, GO)

– Hands-on: Pathways (Mapman) –> abiotic/biotic stresses

– Orthologs (?)

– WGCNA: introduction and examples

– Summary of workshop

-Concepts in Plant Metabolomics

-Bioinformatic tools/softwares for data analysis

-Bioinformatic tools/softwares for data analysis

-A case study: metabolomic profiles of seeds

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