Agenda, resources and other useful information
Why are we here?
What are your expectations?
What do you need Galaxy for?
What would you like to take home from the course?
Utilize Galaxy to upload data, employ tools, view project histories, and execute workflows.
Employ statistical and scatterplot analysis to explore datasets.
Proficiently manage data, including conversion, reformatting, filtering, and sorting of text-based information.
Understand and interpret NGS quality metrics, identify common sequencing artefacts, and apply appropriate quality filtering and trimming strategies to improve raw read datasets.
Perform de novo assembly of bacterial genomes from Illumina reads, assess assembly quality using standard metrics (e.g., N50, contiguity, completeness), and interpret assembly statistics.
Annotate draft bacterial genomes, identify coding sequences and genomic features, evaluate annotation outputs, and visualize annotated elements for biological interpretation.
Detect and characterize antimicrobial resistance (AMR) genes, determine their genomic context (chromosomal vs plasmid), and interpret their clinical and epidemiological relevance.
Identify pathogens and resistance determinants using curated databases (e.g., ABRicate), compare results across multiple samples, and summarize findings in a reproducible framework.
Perform pangenome analysis across multiple bacterial strains, distinguish core and accessory genomes, and interpret gene presence/absence patterns in an evolutionary and functional context.
Conduct microbial variant calling against a reference genome, identify SNPs and small indels, apply filtering criteria, and interpret genomic variation in relation to strain diversity and adaptation.
The computing resources for this training have been provided by the CRS4 datacenter
You will receive all the details to connect to Galaxy Instance: https://omega.crs4.it
In some sections of the course, participants may also need to use public Galaxy instances for specific tools or datasets:
| Title | Lecture / Practical |
|---|---|
| Galaxy at a Glance | Lecture |
| Introduction to Galaxy Analyses | Lecture / Practical |
| Exploring datasets with statistics and scatterplots | Practical |
| Quality Control | Practical |
| Genome Assembly of a bacterial genome (MRSA) | Practical |
| Bacterial Genome Annotation | Practical |
| Identification of AMR genes in an bacterial genome | Practical |
| Pathogen detection with ABRicate | Practical |
| Pangenome Analysis | Practical |
| Microbial Variant Calling | Practical |
| Get Data | Lecture |
| From NCBI’s Sequence Read Archive (SRA) to Galaxy | Practical |
| Data Manipulation | Practical |
| Checking expected species and contamination in bacterial isolate | Practical |
| Introduction to Visualizations in Galaxy | Lecture/Practical |