Agenda, resources and other useful information

A brief introduction to Galaxy. What is Galaxy? Why should you use Galaxy? How do you use Galaxy?

How to get started in Galaxy. Here we'll cover the core tasks in Galaxy: uploading files, using tools, viewing histories, and running workflows.

Often, 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

Introduction to quality control of NGS raw data: key quality metrics, common issues, and strategies to improve dataset quality.

Bacterial genome assembly from Illumina MiSeq reads, covering data quality assessment, assembly generation, and assembly quality metrics.

Annotation and exploration of a draft bacterial genome, including gene prediction, identification of genomic components, evaluation of annotation results, and visualization of annotated features.

Identification and visualization of antimicrobial resistance genes in a bacterial genome, including their genomic location and association with plasmids.

Identification of pathogens from sequencing data and tracking their presence across multiple samples.

If 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.

How do we detect differences between a set of reads from a microorganism and a reference genome?

Optional resources and tutorials to help you get more confident with Galaxy and its everyday usage.

From raw reads to insights: A hands-on guide to bacterial genomics