Objectives

This training session, in webinar, is designed to help you to deal with NGS data of 16S, 18S, ITS, COI, and other DNAs produced with MiSeq/HiSeq from Illumina technologies in the Galaxy workbench. You will discover how to use a Galaxy instance, run bioinformatics analysis on your data (clean reads, clusterize them, do the taxonomic affiliation, etc.) and perform statistics to interpret your results with the FROGS pipeline. With FROGS you can also make functional inference and hypothesize what metabolic functions are present in a microbial community.

Biologists interested in microbiota from various environments (intestinal, soil, aquatic, food, etc.) use genetic markers to know their composition and follow their evolution - metabarcoding. FROGS is a software package for accurate, simple and robust processing of metabarcoding sequencing reads. FROGS uses standard methods and tools combined with original and innovative approaches (such as the support of yeast and fungal markers). FROGS offers in addition to the expected outputs (abundance table of the species in the environment and their affiliations), numerous graphs and statistics allowing biologists an enriched support of their analyses. Its use is open to both non-experts and experts thanks to the launch of the tools via the Galaxy platforms or via the command line.

Our goal is to enable future FROGS users to become self-sufficient in using the tools provided and interpreting the results obtained.

FROGS training documentations and training data : Formation data and documentation

N.B. :The training is conducted in French.

Trainers

Géraldine PASCAL: Research engineer in bioinformatics at INRAE at GenPhySE lab in Toulouse. Coordinator of the FROGS project. Specialists in metabarcoding and metagenomics tools.

Lucas AUER: Reasearch engineer in biostatistics at INRAE at IAM (Tree-microbe interactions) lab in Nancy. Specialist in fungal meta-omics approaches in soils.

Schedule

This training focuses on practice. The 4 days run from 9am to 4.30pm. 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, (v) probable metabolic functions of the studied environment and (vi) build workflow.

• 1 Bioinformatics analysis (Day-1 & Day-2): 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.
• 2 Statistics analysis (Day-3): import and manipulate data, measuring diversity: Alpha, Beta, Unifrac, Bray Curtis, etc., ordination and dimension reduction: MDS, clustering and heatmap, comparing samples: PERMANOVA, adonis. Differential analysis with DeSeq2.
• 3 Functional inference (Day-4): what metabolic functions are present in a microbial community?
• 4 ITS data manipulation (Day-4): what’s the difference?
• 5 And workflow constructions (Day-4)

No pre-requisites are required

Training fees