First Workshop On Pangenomics Algorithms for Omics Data

June 21st, 2019

Univ. Milano-Bicocca. U6 Building – Room Martini (floor -1).

Theme and scope

Computational Pangenomics wants to produce the computational tools for transitioning from a sequence-based genome to graph-based reference genomes, where variants of huge cohorts are represented in a unified way.

Transcriptomics was the first field where the need of imposing a structure over strings has become clear, leading to the notion of a splicing graph to represent all possible transcripts of a gene, as well as the exon-intron structure.

Genome assemblers are increasingly aware that a diploid organism has two different, but very similar, copies of each genome: hence the correct outcome of an assembly cannot be a single string. Finally, metagenomics studies different species that can share portions of the genome: another example where the correct representation of an assembly cannot be linear. Moreover, the 1000 Genomes project has generated new interest in the analysis of a population genome.

The workshop had a previous edition in 2016 focused on Graph assembly algorithm. This time the main aim of the workshop is to bring together researchers that can collaborate on some open problems on graph-based algorithmic approaches to bioinformatics common topics in Bioinformatics.  This year the plan is to apply for the COST program. Since the aim is also stimulate new collaborations, this edition will be mainly focused on the discussion of open problems. To this purpose, part of the day will be focused on the creation of small working groups with each working on an open problem.

Please fill in the registration form if you are interested in participating.


  • 10.00 Broňa Brejová (Comenius University): Differential nanopore coverage analysis through k-mers
  • 10.25 Travis Gagie (Univ. Diego Portales): Report from Dagstuhl 19241
  • 10.50 Fabio Vandin (Univ. Padova): Fast Approximation of Frequent k-mers and Applications to Metagenomics
  • 11.15 Coffee break
  • 11.30 Iman Hajirasouliha (Weill Cornell Medical College): Novel algorithms and applications of Linked-Read genomics and metagenomics (slides)
  • 12.05 Erik Garrison (UCSC): Untangling the pangenome (slides)
  • 12.40 Lunch
  • 14.15 The COST proposal
  • 14.30 Open problems
  • 15.00 Group work on open problems
  • 17.00 Summary of the group work
  • 17.30 Closing

Nonexclusive list of relevant topics

  • graph assembly
  • variation graphs
  • de Bruijn graphs
  • string graphs
  • alternative splicing
  • metagenomics
  • the population genome
  • pan-genome graph
  • graph fragment assembly

Venue and accommodation

The workshop will take place in Milano, at the U6 building (Edificio U6). The building is close to the Bicocca underground station (MM5).

Milan is easily reachable by all major European and main international airports.

The suggested hotels are Starhotel Tourist and Hotel Arcimboldi that are both within a 5-minute walk from the workshop site.

Scientific Committee:

Paola Bonizzoni (
Gianluca Della Vedova (
Marco Previtali (
Raffaella Rizzi (

Author: Gianluca Della Vedova