Where you'll apply the knowledge and techniques you've acquired throughout the previous modules.
Welcome and introductionAgenda, resources and other useful information
Galaxy at a GlanceA brief introduction to Galaxy. What is Galaxy? Why should you use Galaxy? How do you use Galaxy?
Introduction to Galaxy AnalysesHow to get started in Galaxy. Here we'll cover the core tasks in Galaxy: uploading files, using tools, viewing histories, and running workflows.
Exploring datasets with statistics and scatterplotsOften, one or more data pre-processing step(s) may be required to proceed with the analysis. And, after the analysis, maybe you would like to visualize the result or datasets
Data ManipulationHow can I do basic data manipulation in Galaxy? Which tools are available to convert, reformat, filter, sort etc my text-based data?
Introduction to MetagenomicsWhy study the microbiome? Amplicon and shotgun sequencing. Analysis pipelines and Visualisation options
Analyses of metagenomics dataHow to analyze metagenomics data? What information can be extracted of metagenomics data? What is the difference between amplicon and shotgun data? What are the difference in the analyses of amplicon and shotgun data?
16S Microbial Analysis with MothurWhat is the effect of normal variation in the gut microbiome on host health?
Introduction to Visualisations in GalaxyVisualizations are vital for the interpretation of large datasets. Galaxy has numerous visualization options available.
Genomic Data Visualisation with JBrowseHow can I visualise features or blast data? How can I visualise sequencing data in a workflow? Build several visualisations in JBrowse. Have basic familiarity with moving around JBrowse, and loading several data tracks
From NCBI's Sequence Read Archive (SRA) to GalaxyHow can you download public sequencing data deposited in the NCBI Sequence Read Archive (SRA) into a Galaxy history for analysis?
Quality ControlHow to perform quality control of NGS raw data? What are the quality parameters to check for a dataset? How to improve the quality of a dataset?
Taxonomic Profiling and Visualization of Metagenomic DataWhich species (or genera, families, …) are present in my sample? What are the different approaches and tools to get the community profile of my sample? How can we visualize and compare community profiles?
Assembly of metagenomic sequencing dataWhy metagenomic data should be assembled? What is the difference between co-assembly and individual assembly? What is the difference between reads, contigs and scaffolds? How to assess the quality of metagenomic data assembly?
Genome annotation with ProkkaHow can we annotate a bacterial genome? How can we visualize annotated genomic features?
Microbial Variant CallingHow do we detect differences between a set of reads from a microorganism and a reference genome?
Pangenome AnalysisIf we analyse DNA from several bacterial strains, we may want to know which genes they have in common and which are unique to some strains.
Pathogen detectionHow to identify pathogens using sequencing data? How to track the found pathogens through all your samples datasets?
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Some of the materials used in this training are from the Galaxy community and are the result of a collaborative work. Thanks to all the contributors and the Galaxy Training Network!
