| DAY 1 |Sharpening your pencils*(main tutors: Allegra Via and Vincenza Colonna)*
| ------------- |-------------| -----|
| 09:30 | Welcome session: Introduction to the course, participants and instructors |
|10:30| Lecture and practicals: connection to cluster and file transfer|
|11:00| Coffee break|
|11:30| Lecture: Unix|
|12:30| Lunch|
|13:30| Practicals: Unix
|15:00| Coffee break
|15:30| Lecture and practicals: R
|17:00| Lecture: Vincenza Colonna - “NGS and population genomics”
|18:00| End of day1
| DAY 2 |The ABC of NGS (main tutor: Chiara Batini)
| ------------- |-------------| -----|
|09:00| Recap session
|09:30| Lecture: Introduction to NGS technologies and library preparation
|11:00| Coffee break
|11:30| Lecture and practicals: Introduction to data types and data QC
|13:00| Lunch
|14:00| Coffee break
|14:00| Introduction to projects and division in groups, with a cup of coffee
|16:00| Projects - DataQC
|17:30| Recap session
|18:00| End of day2
|19:30| Social dinner @La Campagnola
| DAY 3 |Editing and polishing your draf (main tutor: Chiara Batini)
| ------------- |-------------| -----|
|09:30| Lecture and practicals: Mapping; SAM/BAM format
|11:00| Coffee break
|11:30| Lecture and practicals: BAM refinement [Local Realignment, Base quality recalibration]
|13:00| Lunch
|14:00| Lecture and practicals: BAM refinement [Duplicate removal, BAM handling, BAM visualization]
|16:00| Coffee break
|16:30| Projects - alignment
|17:30| Recap session
|18:00| End of day3
| DAY 4 |Spot the difference (main tutor: Chiara Batini)
| ------------- |-------------| -----|
|09:00| Recap session
|09:30| Lecture and practicals: Variant calling - SNPs
|11:00| Coffee break
|11:30| Lecture and practicals: Filtering variants
|13:00| Lunch
|14:00| Projects - BAM refinement and visualization
|16:00| Coffee break
|16:30| Projects - variant calling
|17:30| Recap session
|18:00| End of day4
| DAY 5 | Down to business (main tutor: Vincenza Colonna)
| ------------- |-------------| -----|
|09:00| Recap
|09:30| Projects - Variant filtering
|11:00| Coffee break
|11:30| Projects - Evolutionary analyses
|13:00| Lunch - Pizza
|14:30| Projects - discussion and preparation of final results
|16:00| Coffee break
|16:30| Presentation and discussion of results
|17:30| Recap: Course wrap-up and feedback
|18:00| End of day5