Welcome and introduction
Agenda, resources and other useful information
Welcome!
-
Why are we here?
-
What are your expectations?
-
What do you need Galaxy for?
-
What would you like to take home from the course?
Learning outcomes
- 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.
- Determine the most suitable approach for metagenomic data analysis.
- Discriminate between tools suited for amplicon and shotgun data analysis.
- Effectively visualize community structures.
- Execute 16S rRNA sequencing analysis within Galaxy using the mothur toolsuite.
- Assess sequencing experiment error rates via mock community data.
- Master the visualization of sample diversity through Krona and Phinch tools.
- Execute rigorous quality control of NGS raw data.
- Extract comprehensive community profiles from microbiome datasets.
- Proficiently reconstruct microorganism genomes within sampled communities.
- Evaluate the quality of metagenomic assemblies.
- Skillfully annotate bacterial genomes.
- Visualize and interpret annotated genomic features.
- Identify variants between reference genomes and read datasets.
- Interpret SNP data within the context of read alignments to the genome.
- Analyze the impact of variants on genomic features.
- Detect pathogens by identifying virulence factor gene products.
- Characterize strains and identify antimicrobial resistance genes within your samples.
Go Up
Computing resources
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://izs3.crs4.it
Go Up
Agenda
April 18-20, 2023
| Title |
Lecture / Practical |
| Galaxy at a Glance |
Lecture |
| Introduction to Galaxy Analyses |
Lecture / Practical |
| Exploring datasets with statistics and scatterplots |
Practical |
| Data Manipulation |
Practical |
| Introduction to Metagenomics |
Lecture |
| Analyses of Metagenomics Data |
Lecture / Pracctical |
| 16S Microbial Analysis with mothur |
Practical |
September 26-28, 2023
| Title |
Lecture / Practical |
| Introduction to Visualisations in Galaxy |
Lecture |
| Genomic Data Visualisation with JBrowse |
Practical |
| From NCBI’s Sequence Read Archive (SRA) to Galaxy |
Practical |
| Quality Control |
Practical |
| Taxonomic Profiling and Visualization of Metagenomic Data |
Lecture / Practical |
| Assembly of metagenomic sequencing data |
Lecture / Practical |
| Genome annotation with Prokka |
Lecture / Practical |
| Microbial Variant Calling |
Lecture / Practical |
| Pangenome Analysis |
Lecture / Practical |
| Pathogen Detection |
Lecture / Practical |
| Hands-On |
Practical |
Go Up
