Course Description
Participants will learn about pangenome concepts and gain practical experience building and analyzing pangenome graphs. They will apply these methods to complex research questions that require understanding the relationships between multiple genomes or accounting for variability when analyzing new genomes. By the end of the practical course / workshop, participants will have a strong understanding of pangenome methods based on whole genome assemblies.
Important Dates
Deadline for applications: 24 May 2024
Chosen participants will be notified by: 31 May 2024
Course date: 19-21 June 2024
Fee
The course includes a fee of 70€ which covers coffee-breaks. Participants are expected to pay their own travel and accomodation costs (if any).
Selection
A maximum of 24 candidates will be selected based on their need for the course as emerging from the application form. Chosen participants will be notified by 17th May 2024. Priority will be given to candidates from ELIXIR-IIB member institutes (see the list at the bottom) and ELIXIR Nodes. Go to the Application Form – Registration.
Cancellation policy: Attendance is limited to 24 participants. We expect many more applications. Accepted participants commit to attend the course for its whole duration. Failure to attend training sessions is disruptive. Moreover, it blocks other candidates from participating. Therefore, a cancellation policy is in place so that only written requests presented 10 days in advance relatively to the course starting date are accepted.
Instructors
- Erik Garrison – University of Tennesse Health Science Center
- Andrea Guarracino – University of Tennesse Health Science Center
Helpers
- Flavia Villani – University of Tennesse Health Science Center
Organisers
- Vincenza Colonna – University of Tennesse Health Science Center
- Erik Garrison – University of Tennesse Health Science Center
- Andrea Guarracino – University of Tennesse Health Science Center
- Luana Licata Tor Vergata University of Rome – ELIXIR-IT
- Flavia Villani – University of Tennesse Health Science Center
Contact
For all kinds of queries, please contact the local organiser Luana Licata at: luana.licata@gmail.com. For questions about course content, methods, and materials, please contact Erik Garrison egarris5@uthsc.edu and Andrea Guarracino aguarra1@uthsc.edu.
Learning outcomes
By the end of this course, learners will be independently able to:
- Understand the concepts and importance of pangenomics in addressing reference bias and capturing genome variability.
- Apply pangenome methods to complex research questions that require understanding the relationships between multiple genomes or accounting for variability when analyzing new genomes.
- Gain practical experience in building pangenome graphs from whole-genome assemblies using tools like PGGB and ODGI.
- Learn how to analyze and interpret pangenome graphs
Course prerequisites
The participants will need to have some experience in Linux command line (bash), enough to start tools and find paths to files. Experience with Next Generation Sequencing data and common file formats (fasta, fastq, bam, etc.) will be extremely useful, but is not mandatory.
Registration
After selection, confirmed participants will be able to access the course agenda, materials and communication tools on the ELIXIR-SI eLearning Platform (EeLP).