Keywords: Galaxy, NGS, one-health, training, tuberculosis

Learning objectives:

• Be able to read and interrogate a phylogeny encountered in the literature
• Calculate pairwise SNP distances between MTB samples
• Create a SNP alignment
• Familiarize yourself with the basics of Galaxy
• How can we predict drug resistance from those variants
• How do we annotate those variants
• How should we filter those variants
• Identify transmission clusters based on SNP distances
• Learn how histories work
• Learn how to create a workflow
• Learn how to extract and run a workflow
• Learn how to obtain data from external sources
• Learn how to run tools
• Learn how to share a history
• Learn how to share your work
• Learn how to upload a file
• Learn how to use a tool
• Learn how to view histories
• Learn how to view results
• Study the emergence and spread of drug resistance based on transmission analysis.
• Understand the basic concepts behind phylogenetic trees, as applied to Mycobacterium tuberculosis

Organizer: Andrea Cabibbe (https://training.galaxyproject.org/training-material/hall-of-fame/andreacabibbe/), Andrea Spitaleri (https://training.galaxyproject.org/training-material/hall-of-fame/andrea-spitaleri/), Arash Ghodousi (https://training.galaxyproject.org/training-material/hall-of-fame/arashghodousi/), Christoph Stritt (https://training.galaxyproject.org/training-material/hall-of-fame/cstritt/), Daniela Brites (https://training.galaxyproject.org/training-material/hall-of-fame/dbrites/), Galo A. Goig (https://training.galaxyproject.org/training-material/hall-of-fame/GaloGS/), Liliana Rutaihwa (https://training.galaxyproject.org/training-material/hall-of-fame/lilianarutaihwa/), Peter van Heusden (https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/)

Event types:

• Workshops and courses

Sponsors: IRCCS Ospedale San Raffaele, LINQ management GmbH, Pan-Africa network for genomic surveillance of poverty related diseases and emerging pathogens, Pan-African Consortium for the Evaluation of Antituberculosis Antibiotics, South African National Bioinformatics Institute, University of the Western Cape, Swiss Tropical and Public Health Institute, The European & Developing Countries Clinical Trials Partnership, The European Union, The Foundation for Innovative New Diagnostics, Università Vita-Salute San Raffaele

Scientific topics: Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease, DNA polymorphism, Phylogeny