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Metabarcoding analyses (using FROGS and Phyloseq)This course offers an introduction to metabarcoding analyses at two different levels/steps: bioinformatics with FROGS pipeline in the Galaxy environment, biostatistics with PhyloSeq R package. This includes preprocessing, clustering and OTU picking, taxonomic assignation, estimation of diversity, visualization of statistics results. |
Prerequisites
Galaxy, R knowledge, Linux
Program
- Introduction to metagenomics and metabarcoding
- Pre-processing, Clustering, taxonomic affiliation (FROGS)
- Handling and visualizing OTU table using (FROGSSATS and PhyloSeq R package (PhyloSeq)
Learning objectives
- Manipulate tools available for metabarcoding analysis
- Study sample diversity by using NGS and post-NGS analysis tools
- Visualize diversity metrics in metabarcoding approach
Instructors
- Julie Reveilleud (JR) - julie.reveillaud@inra.fr
- Frederique Mahé (FM) - frederic.mahe@cirad.fr
- Florentin Constancias (FC) - florentin.constancias@cirad.fr
- Julie Orjuela (JO) - julie.orjuela@ird.fr
- Marie Simonin (MS) - marie.simonin@ird.fr
- Alexis Dereeper (AD) - alexis.dereeper@ird.fr
- Aurore Comte (AC) - aurore.comte@ird.fr
Trainings
| Date | Location | Topics | Participants | Instructors | Links | Units |
| 2019 | Montpellier, France | Introduction to transcriptomics analyses | 20 | FM, FM, JO, JR, MS | UMR ASTRE, BGPI, DIADE, IPME | |
| 2018 | Montpellier, France | Introduction to transcriptomics analyses | 20 | FC, JO, AD | UMR DIADE, IPME, BOREA, QUALISUD | |
| 2016 | Ouagadougou, Burkina | Bioinformatics applied to genomics | 20 | FM, AD | IRD | |
| 2015 | Hanoi, Vietnam | Bioinformatics applied to genomics | 20 | AD | LMI Rice |