Practicals in next generation sequencing
Responsable : Marie Sémon
3 crédits ECTS, 36h de TP
NGS (Next Generation Sequencing) refers to high-throughput DNA sequencing technologies that generate a very large number of nucleic sequences. There are many applications (RNA-seq, metagenomics, resequencing, ChIP-seq…) that are used today in many fields of biology, such as cancerology, development, microbiology, epigenetics, evolution, and ecology. In this context, the main objective of this course is to show the practical use of NGS, from the sample, to the final results, via library preparation, sequencing, and bioinformatics analysis.
Each group of students will be in charge of two small projects, chosen among several concrete applications whose list will depend on the year and/or on the interests of the students, and will reflect several disciplines. The first project will be an application using metagenomics (from the sample to the result, for instance, studying the diversity of intestine microbiotes in drosophila), and the second project, an application using RNA-seq (restricted to the bioinformatics analysis, for instance the rose flower). During the practical courses, the discussion of methodological choices with other students and teachers will be encouraged (experimental settings, choices of tools, interpretation of the results). A workshop will be organised at the end of the session so that each group can present and discuss its results. No prerequisite in bioinformatics is necessary ; all tools will be used through Galaxy and R. NGS sequencing is made available
through the sequencing platform of the IGFL.