The event took place on September 5–9, 2022 at Hasso-Plattner-Institut in Potsdam. The workshop was organized by Bielefeld University and held jointly with WABI 2022 and PANGAIA workshop.

The program covered topics foreseen in the ALPACA Grant Agreement which are:

Three half-days will be dedicated to scientific courses, one half-day to the soft-skills course. Other activities will include business meeting (afternoon of day 1), hackathon (afternoon of day 3), and problem sessions (evenings). The preliminary topics of the courses:

(i) Metagenome assembly and analysis (R.Chikhi IP, 1 ECTS); (ii) Latest pan-genome research trends (seminars by advisory board members, 0.5 ECTS); (iii) Soft-skills: Improving research impact with social media presence (P. Peterlongo INRIA, 0.5 ECTS), (iv) Peer Community in bioinformatics: a new approach to reviewing and publishing (C. Scornavacca, CNRS, 0.5).


(Program on WABI website and in PDF)

Pangenome sequencing and analysis

All timings shown are Central Europe Summer Time (CEST)
Monday, September 5
10:10 – 11:10WABI Session on k-mer Sets
14:00 – 15:00WABI Session on Succinct Data Structures
Tuesday, September 6
8:50 – 9:50WABI Session on BWT-like Data Structures
Wednesday, September 7
8:50 – 9:50WABI Session on Indexing Genomes
11:30 – 12:30Leena Salmela
Efficient solutions to biological problems using de Bruijn graphs
14:00 – 15:00Knut Reinert
Hierarchical Interleaved Bloom Filter: Enabling ultrafast, approximate sequence queries
ALPACA business meeting (Alexander Schönhuth)
15:20 – 16:20PANGAIA network meeting, part I (Paola Bonizzoni)
16:30 – 21:30Social event
Boat tour including dinner and drinks (register by email to jens.stoye[at]uni-bielefeld[dot]de)
Thursday, September 8
8:50 – 9:50PANGAIA network meeting, part II (Paola Bonizzoni)
10:10 – 11:10Camille Marchet
Round table discussion: how to improve communication with your advisors, and a few other items about wellness at work
Mathias Weller
Peer Community in bioinformatics: a new approach to reviewing and publishing
11:30 – 12:30Christina Boucher
Computational Problems in Metagenomic Amplification
14:00 – 15:00Erin K. Molloy
Recent advances and open challenges in estimating evolutionary histories from low-homoplasy markers
Rayan Chikhi
Metagenome assembly and analysis
15:20 – 16:20Paul Medvedev
The theoretical analysis of sequencing bioinformatic algorithms
16:40 – 18:00Open problems session (Travis Gagie)
Friday, September 9
8:50 – 9:50Hackathon, part I (Rayan Chikhi)
10:10 – 11:10Hackathon, part II (Rayan Chikhi)
11:30 – 12:30Gene Myers
High Fidelity Genome Sequencing: What have we been missing?
Closing remarks


Building H, Room 2.57, Hasso-Plattner-Institut (HPI), Potsdam, Germany

Annual Workshop 2: “Pan-genome sequencing and analysis”