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Training courses Computational Pangenomics


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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


Venue

Aula informatizzata, 2nd Floor, Building CU010, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy link to the map

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.

Target audience

This course is aimed at PhD-students, post docs or other researchers interested in learning about pangenomics. It will be especially useful for researchers that have (or will have) data of their own.

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

Application Form

After selection, confirmed participants will be able to access the course agenda, materials and communication tools on the ELIXIR-SI eLearning Platform (EeLP).

Programme

Wednesday - 19 June
09:00 - 10:00 Lecture Erik Garrison Introduction to pangenomics
10:00 - 10:30 Break
10:30 - 12:00 Practical Everyone HLA & LPA graph building
12:00 - 13:30 Lunch break
13:30 - 14:00 Lecture Andrea Guarracino Understanding pangenomes
14:00 - 15:00 Practical Everyone Human pangenome graph building
15:00 - 15:30 Break
15:30 - 17:00 Practical Everyone ODGI applications

Thursday - 20 june
09:00 - 10:00 Lecture + Practical Everyone Discussion about previous day activities
10:00 - 10:30 Break
10:30 - 12:00 Practical Everyone Yeast pangenome graph building
12:00 - 13:30 Lunch break
13:30 - 14:00 Lecture Andrea Guarracino Long-read Assembly
14:00 - 15:00 Practical Everyone Assembly and QC
15:00 - 15:30 Break
15:30 - 17:00 Practical Everyone Assembly and pangenome graphs

Friday - 21 june
09:00 - 10:00 Lecture + Practical Everyone Discussion about previous day activities
10:00 - 10:30 Break
10:30 - 12:00 Wrap-up and feedback session

ELIXIR-IIB member institutes

  1. CNR, National Research Council (Lead Institute)
  2. CRS4
  3. CINECA
  4. Edmund Mach Foundation, Trento
  5. ENEA
  6. Fondazione Telethon
  7. INFN
  8. Istituto Superiore di Sanità (ISS)
  9. GARR
  10. Stazione Zoologica Anton Dohrn, Napoli
  11. University of Roma “Sapienza”
  12. University of Bari
  13. University of Bologna
  14. University of Firenze
  15. University of Milano
  16. University of Milano Bicocca
  17. University of Napoli
  18. University of Padova
  19. University of Parma
  20. University of Roma “Tor Vergata”
  21. University of Salerno
  22. University of Torino
  23. University of Tuscia