FROGS formation : tools for bioinformatics and statistics analyses with amplicon metagenomics data

FROGS formation : tools for bioinformatics and statistics analyses with amplicon metagenomics data (29/11/2021 - 02/12/2021)

The Toulouse Genopole bioinformatics platform, Sigenae and NED (GenPhySE) organize a series of training courses to familiarize yourself with the various resources it provides. These resources are currently: the hardware infrastructure, biological data banks and widely used bioinformatics softwares. This training session, organized by Bioinfo Genotoul, Sigenae and NED (GenPhySE), is designed to help you to deal with NGS data of 16S, 18S, ITS … DNA produced with MiSeq from Illumina and Roche 454 technologies in the Galaxy workbench. You will discover how to use our Galaxy instance, clean reads, clusterize them, do the taxonomic affiliation and perform statistics to interpret your results with the FROGS pipeline (http://frogs.toulouse.inrae.fr/).

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This training focuses on practice.

The 4 days run from 9am to 5pm. After a first introductory session on the proper use of Galaxy and preparation of datasets, you will learn how to use the FROGS software. At the end of the training, you will know (i) evaluate your datasets, (ii) how to interpret the results in the table of abundance, (iii) use main statistical tools, (iv) manipulate 16S and ITS datasets and (v) build workflow.
 

  • Part 1: on 16S datasets, we manipulate FROGS tools for : data preprocessing, clustering, graphical interpretations, removal chimera step, filtering step, using tools for results visualization and affiliation step.

  • Part 2: Statistics analysis FROGS tools : import and manipulate data, measuring diversity: Alpha, Beta, measuring diversity: Unifrac, Bray Curtis, etc., ordination and dimension reduction: MDS, clustering and heatmap, comparing samples: PERMANOVA, adonis. Differential analysis with DeSeq2.

  • Part 3 : ITS data manipulation, what’s the difference ? And workflow constructions.

 

The session will take place in the room ‘salle de formation’ at INRA center of Toulouse-Auzeville.

WARNING COVID19 : This session will take place remotely via the zoom tool.

 

Training materials (Slides, exercises and corrections) will be given to you during the session.

 

Slides and exercises.

 

Bookings: FROGS formation : tools for bioinformatics and statistics analyses with amplicon metagenomics data

Bookings have closed for this event.