Summary

The first summer school took place in July 4–8, 2022 at Villa del Grumello, Como in Italy. The school was organized by the University of Milano-Bicocca. More information can be found on the website dedicated to the school.

The proposed program in the ALPACA Grant Agreement was a 4-day school covering the following topics:

Preliminary course topics: (i) Data structures for genomic variants (R.Durbin UCAM, T.Marschall UDUS, 0.5 ECTS), (ii) Pan-genome storage and search (J.Stoye UNIBI, 1 ECTS); (iii) Alignments of pan-genome graphs (V.Mäkinen UHEL, 1 ECTS); (iv) Research dissemination, open science and open access (T.Marschall UDUS, 0.5 ECTS); (v) Project management (J.Budiš GENETON, 0.5 ECTS); (vi) Scientific writing and research dissemination (A.Schönhuth UNIBI, 0.5 ECTS).

The school will include a multi-session hackathon where groups of participants will analyze pan-genomic data sets provided by non- academic partners (analysis leaders B.Brejová UK BA, J.Budiš GENETON, T.Marschall UDUS)

Schedule

Monday, July 4

  • Welcome and Registration

  • Lunch

  • Veli Mäkinen

  • Coffee break

  • Pjotr Prins

Tuesday, July 5

  • Jouni Siren

  • Coffee break

  • Zamin Iqbal

  • Lunch

  • Mareike Fischer

  • Coffee break

  • Tomáš Szemes

Wednesday, July 6

  • Jouni Siren

  • Coffee break

  • Evan Eichler

  • Lunch

  • Rayan Chikhi

  • Coffee break

  • Erik Garrison

Thursday, July 7

  • Veli Mäkinen

  • Veli Mäkinen

  • Coffee break

  • Coffee break

  • Christina Boucher

  • Christina Boucher

  • Lunch

  • Lunch

  • Jasmijn Baaijens

  • Jasmijn Baaijens

  • Coffee break

  • Coffee break

  • Alexander Schönhuth

  • Alexander Schönhuth

Friday, July 8

  • Shilpa Garg

  • Shilpa Garg

  • Coffee break

  • Coffee break

  • Alexander Schönhuth

  • Alexander Schönhuth

  • Lunch

  • Lunch

  • Departures

  • Departures

Program

All timings shown are Central Europe Summer Time (CEST)

Monday, July 4
14:00-15:30Veli Makinen (Univ Helsinki)
Alignments on pangenome representations
16:00-18:00Pjotr Prins (Univ. Tennessee)
why free software matters for Science and what to do
Tuesday, July 5
9:00-10:30Jouni Siren (Univ. California Santa Cruz)
Pangenome graphs with haplotype paths
11:00-12:30 Zamin Iqbal (EMBL)
Analysis of genetic variation with genome graphs
14:00-15:30 Mareike Fischer (Univ. Greifswald)
How future-proof are phylogenetic methods?
16:00-18:00 Tomas Szemes (Geneton)
Bioinfomatics-driven genomic biotechnologies and how they help in solving biomedical challenges
Wednesday, July 6
9:00-10:30 Jouni Siren (Univ. California Santa Cruz)
Pangenome graphs with haplotype paths
11:00-12:30 Evan Eichler (Univ. of Washington)
Long-read sequencing and the structural diversity of human genomes
14:00-15:30 Rayan Chikhi (lnstitut Pasteur)
Introduction to sequence graphs representations
16:00-18:00 Erik Garrison (Univ. Tennessee)
Building and understanding pangenome variation graphs
Thursday, July 7
9:00-10:30 Veli Makinen (Univ Helsinki)
Alignments on pangenome representations
11:00-12:30 Christina Boucher (Univ. of Florida)
Understanding the details behind Moni Align
14:00-15:30 Jasmijn Baaijens (TU Delft)
Viral quasispecies assembly
16:00-18:00 Alex Schoenhuth (Univ. Bielefeld)
Introduction to Capsule networks
Friday, July 8
9:00-10:30 Shilpa Garg (Univ. of Copenhagen)
Chromosome-scale haplotype-resolved assembly
11:00-12:30 Alex Schoenhuth (Univ. Bielefeld)
Introduction to Capsule networks
Summer School 1: “Algorithmic techniques in pan-genomics”