Program

14:00-14:30 Introduction to the workshop 

14:30-16:00 Introduction to UNIX (Practical; Mirko Martini)

16:00-16:30 Coffee break

16:30-18:00 Introduction to GitHub (Practical; Mirko Martini)

18:00-20:30 Participants 1' presentations & Social gathering

09:30-10:30 History of the pangenome concept from bacteria to the human pangenome (Theory; Secomandi & Gallo)

10:30-11:00 Coffee break

11:00-12:30 Introduction to the concepts and available pipelines for genome assembly, pangenome graphs construction and downstream analyses (Practical; Secomandi & Gallo)

12:30-14:00 Lunch break

14:00-16:00 Pangenome construction, evaluation and visualization (Practical; Secomandi & Gallo) 

16:00-16:30 Coffee break

16:30-18:00 Downstream analyses and future prospects of pangenomics, with open discussion (Practical; Secomandi & Gallo)

18:00-19:30 Social cocktail with the speaker 

09:30-10:30 Fundamentals of population genetics to understand the links between micro and macro evolutionary processes (Theory;  Chiara Barbieri)

10:30-10:45 Coffee break

10:45-13:00 Guided exercises on introduction to population genetics (PCA, Admixture, genetic distances) confronting patterns of genetic diversity with other aspects of human cultural evolution, like linguistic diversity (Practical; Chiara Barbieri)

13:00-14:00 Lunch break

14:00-15:00 Overview of how ancient DNA can be used to study animal domestication, with a specific focus on cats (Felis catus) (Practical; Claudio Ottoni) 

15:00-15:15 Coffee break

15:15-17:30 Reconstruction of the mtDNA phylogeny of ancient and modern cats and explore patterns of ancient gene flow between wild and domestic cats using D- and F- statistics (Practical; Claudio Ottoni)

17:30-18:00 Wrap-up and open discussion

18:00-19:30 Social cocktail with the speakers 

19:30-22:00 Scientific dissemination with board games (Game night; Federico Plazzi)

09:30-11:00 Why are genomes useful for conservation? Introduction to conservation genomics: concepts, challenges, samples and data types (Theory; Clàudia Fontserè)

11:00-11:30 Coffee break

11:30-13:00 Exploratory analysis with low coverage data: Quality control, contamination, mapping success, relatedness, population structure (Practical;  Clàudia Fontserè)

13:00-14:30 Lunch break

14:30-16:00 Genomic erosion, temporal series and demographic analysis: concepts and applications (Theory;  Clàudia Fontserè) 

16:00-16:30 Coffee break

16:30-18:00 Genomic erosion, temporal series and demographic analysis: damage patterns, PCA, admixture, heterozygosity, inbreeding (Theory and Practical;  Clàudia Fontserè)

18:00-19:30 Social cocktail with the speaker

20:00-22:00 Social dinner (optional)

09:30-11:00 Focus on European funds for individual researchers: Marie Skłodowska-Curie Postdoctoral Fellowships (MSCA-PF) and European Research Council (ERC) Starting grants. (Seminar; Elisabetta Boglich Perasti)

11:00-11:20 Coffee break

11:20-13:00 Get straight to the point: tips on making your MSCA application eye-catching! (Practical; Heidi Christine Hauffe)