Related Deliverable

D4.2: Annual Workshop 1 (PDF)


The Annual Workshop 1 was the first training event planned in the Grant Agreement with the delivery date in Month 11. The goal of this event was to introduce and discuss “Challenges of computational pan-genomics” as its title suggests. The program also covers prerequisites essential for the topic as well as soft-skill courses such as Ethics in Research and Gender and Diversity issues.

According to the Grant Agreement, first Annual Workshop is a 3-day event with 2 ETC planned as follows:

Three half-days will be dedicated to scientific courses, and one half-day to the soft-skills course. Other activities will include business meetings (afternoon of day 1), hackathons (afternoon of day 3), and problem sessions (evenings). The preliminary topics of the courses:
(i) Overview of existing methods and tools for pan-genomics (S.Pissis NWO-I, E. Rivals CNRS, J.Stoye UNIBI, 1 ECTS); (ii) Overview of open challenges for pan-genomics (A.Schönhuth UNIBI, R.Durbin UCAM, T.Marschall, UDUS, 0.5 ECTS); (iii) Soft-skills: Ethics in research, research integrity. Gender and Diversity Issues (N.Pisanti UNIPI, P.Bonizzoni UNIMIB 0.5 ECTS)

The workshop took place from November 29 to December 2 in Pisa. The venue was located in the Department of Computer Science at the University of Pisa. The event was organized by the University of Pisa following the same agenda as mentioned above. Four half-day training sessions by the Beneficiaries along with 5 scientific sessions by invited speakers were offered during the event (see Program)

The event was open to the public, however, due to the regulations regarding the COVID-19 pandemic, the number of people present at the venue was limited. Nevertheless, we were able to accommodate many participants including affiliated Ph.D. students and accomplished invited speakers besides the ALPACA core members.

First day of the workshop

One week prior to the workshop two PIs, including the Coordinator, Alexander Schönhuth, had close COVID contacts and refrained from attending the event in person. Unfortunately, Alex tested positive and could not join us online. Consequently, the training session which was supposed to be presented by Alex was replaced by an instructive lecture given by Jens Stoye (UNIBI) about the open/close characteristics of pangenomes. The “ALPACA Community Meeting” which was supposed to be hosted by Alex was subsequently canceled.

We keep all presentations and recorded sessions on the cloud and we provided all members with private links to access the materials of the workshop. The materials are still maintained, although access is limited and will be available upon request.

Photo Gallery


Challenges of computational pan-genomics

All timings shown are Central Europe Summer Time (CEST)
Monday, November 29
9:00-09:30Opening + Icebreaking
9:30-12:40Training Session 1Eric Rivals
Pattern Matching and Alignment


Alexander Schoenhuth
Phased Genome Assembly
12:45-14:45Lunch Break
15:00-16:10Scientific Session 1

[chair: Nadia]
Duccio Medini (GSK-Novartis Vaccines R&D Siena, Italy)
The Pangenome: A Data-Driven Discovery in Biology


Paul Medvedev (Penn State University, USA)
The minimizer Jaccard estimator is biased and inconsistent
16:30-17:10Scientific Session 2
[chair: Alex]
Alessandra Carbone (CNRS & Sorbonne University, France)
A phylogenetic reconstruction based on chromosomal rearrangements and multiple genome comparison
17:10-18:00 ALPACA Community Meeting
[chair: Alex]
18:10 Problems Session
Tuesday, November 30
9:00-12:15 Training Session 2Solon Pissis
Indexing Genomic Sequences


Richard Durbin
Population genetic variation
12:15-14:30 Lunch Break
14:30-15:50 Scientific Session 3
[chair: Richard]
Sandra Smit (Wageningen University, the Netherlands)
Construction and (visual) analytics of pangenomes using PanTools


Fabio Vandin (University of Padua, Italy)
Approximating Frequent k-mers by Sampling, and Applications
15:50-16:10 Break
16:10-17:30 Scientific Session 4
[chair: Eric]
Vincenza Colonna (Institute of Genetics and Biophysics CNR, Italy)
Pangenomics of inbred mice


Benedict Paten (University of California Santa Cruz, USA)
Building and Using Human Pangenomes
17:30 Problems session
Wednesday, December 1
9:00-12:15Training Session 3 Nadia Pisanti
Gender and Diversity Issues


Paola Bonizzoni
Ethics in Research, Research Integrity
12:15-14:30 Lunch Break
14:30-16:00 Scientific Session 5
[chair: Tobias]
Erik Garrison (University of Tennessee Health Science, USA)
Understanding all variation in telomere-to-telomere genome assemblies


Iman Hajirasouliha (Weill Cornell Medicine, USA)
Algorithms and applications of long-range genome sequencing
16:00-evening Problems sessions inside Social Event
Thursday, December 2
9:00-12:15 Training Session 4 Jens Stoye


Tobias Marschall
Open Challenges in Pangenomics
12:15-14:30 Lunch Break
14:30 Problems session
Annual Workshop 1: “Challenges of computational pan-genomics”