CPANG22

Computational PANgenomics

Timetable (provisional)
Mon, May 23rd
Day #1
09:30 - 11:00 Getting to know each other and establishing teamwork
Introduction to the course objectives, and context in bioinformatics
11:00 - 11:30 Coffee Break
11:30 - 12:30 Understanding pangenomes (introduction cont.
12:30 - 14:00 Lunch Break
14:00 - 16:00 Building the pangenome
16:00 - 16:30 Tea Break
16:30 - 18:00 Hello pangenome! (Build your first pangenome.)
Tue, May 24th
Day #2
09:30 - 11:00 Morning Wrap-up (what have we done so far?)
Navigating the pangenome (model, coordinates, vector spaces, )
11:00 - 11:30 Coffee Break
11:30 - 12:30 Navigating the pangenome (cont.)
12:30 - 14:00 Lunch Break
14:00 - 16:00 Visualizing pangenome graphs
16:00 - 16:30 Tea Break
16:30 - 18:00 Applications build graphs for the human MHC, arabidopsis chromosomes, synthetic phages, diverged yeast, helicobacter, and E. coli
Wed, May 25th
Day #3
09:30 - 11:00 Morning Wrap-up (what have we done so far?)
Read mapping to pangenomes
11:00 - 11:30 Coffee Break
11:30 - 12:30 Align a read set
12:30 - 14:00 Lunch Break
14:00 - 16:00 Variant calling in a pangenome
16:00 - 16:30 Tea Break
16:30 - 18:00 Comparing to the linear approach, understanding benefits and limitations with both graph-based and reference based methods
Thu, May 26th
Day #4
09:30 - 11:00 Morning Wrap-up (what have we done so far?)
Using an assembly graph as a reference
11:00 - 11:30 Coffee Break
11:30 - 12:30 Thinking about haplotypes
12:30 - 14:00 Lunch Break
14:00 - 16:00 Show and tell: Discussion of applications relevant to participants
16:00 - 16:30 Tea Break
16:30 - 18:00 End-of-day wrap-up and general discussion of the outcomes
Fri, May 27th
Day #5
09:30 - 11:00 Morning Wrap-up (what have we done so far?)
Long read to graph alignment
11:00 - 11:30 Coffee Break
11:30 - 12:30 Error correction and SV calling
12:30 - 14:00 Lunch Break
14:00 - 16:00 Show and tell: Discussion of applications relevant to participants
16:00 - 16:30 Tea Break
16:30 - 18:00 Final wrap-up and general discussion of the outcomes
Course Homepage

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

GTPB Homepage

IGC Homepage

Last updated: April 26th 2022