Workshop on Graph Assembly Algorithms for omics data

November 18th, 2016

Univ. Milano-Bicocca. Building U24 – Room C02

Theme and scope

New and different sequencing technologies have appeared in the last few years with the promise of overcoming Illumina as the reference platform: PacBio, 10x Genomics, and MinION being the most relevant today. Those technological improvements have shown the limitations of managing linear strings instead of richer models that are usually graph-based. 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.

From a bioinformatics point of view, this results in the need for refining the classical approach where a genome is represented as a single string. Instead, some approaches based on graph representations have become more popular. For instance, some recent developments have been obtained on defining a common format (GFA – Graph Fragment Assembly) to represent an assembly graph.

The aim of this informal workshop is to bring together researchers from different, but correlated, areas under the widest possible notion of graph assembly algorithms, such as genome assembly, alternative splicing prediction, metagenomics, graph manipulation and representation, that are involved in the thorough investigation of these problems with both theoretical and experimental approaches. The goal is to brainstorm which challenges are the most important and can drive the research agenda in the next few years, and to jumpstart a proposal for a European Training Network (specific call) under the Horizon 2020 program and/or a COST action (call).

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

Tentative schedule

9-9.30: Welcome and registration

9.30-11.35: Session 1 (5 talks, 25 minutes each)

  1. Alexander Schoenhuth (Centrum Wiskunde & Informatica). De novo assembly of viral quasispecies using overlap graphs (slides)

  2. Leena Salmela (University of Helsinki). Path searching problems in de Bruijn graphs (slides)

  3. Tomas Vinar (Comenius University). Probabilistic Models for Genome Assembly

  4. Jouni Siren (Wellcome Trust Sanger Institute). Indexing Graphs for Path Queries (slides)

  5. Guillaume Holley (Universität Bielefeld). Bloom Filter Trie: an efficient data structure for colored de Bruijn graphs (slides1 slides2)

11.35-12.00: Coffee break

12.00-13.40: Session 2 (4 talks, 25 minutes each)

  1. Pierre Peterlongo (Université de Rennes 1). Graph assembly algorithms at the Genscale team (slides)

  2. Jean-François Flot (Université libre de Bruxelles). Read compaction from a De Bruijn graph: a new paradigm for polymorphic genome assembly

  3. Rayan Chikhi (CNRS). Efficient construction of compacted de Bruijn graphs (slides)

  4. Rumen Andonov (Université de Rennes 1). Global Optimization Methods for Genome Scaffolding and Completing Genome Assemblies (slides)

13.40-14.30: Lunch

14.30-15.45: Session 3 (3 talks, 25 minutes each)

  1. Tobias Marschall (Universität des Saarlandes). Computational pan-genomics: status, promises and challenges (slides)

  2. Eric Rivals (CNRS). Superstring Graph: an alternative to assembly with multiple de Bruijn graphs

  3. Gianluca Della Vedova (Università di Milano-Bicocca). BWT and Graph Algorithms

15.45-17.30: Discussion

Venue and accommodation

The workshop will take place in Milano, at the Department of Computer Science (DISco), at the U24 building (Edificio U24).

Milan is easily reachable by all major European and main international airports. How to reach us

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

List of speakers

Scientific Committee:

Paola Bonizzoni
Gianluca Della Vedova
Raffaella Rizzi

List of partecipants

  • Rumen Andonov
  • Stefano Beretta
  • Paola Bonizzoni
  • Broňa Brejová
  • Rayan Chikhi
  • Gianluca Della Vedova
  • Guillaume Holley
  • Jean-François Flot
  • Murray Patterson
  • Pierre Peterlongo
  • Nadia Pisanti
  • Alberto Policriti
  • Marco Previtali
  • Eric Rivals
  • Raffaella Rizzi
  • Romeo Rizzi
  • Giovanna Rosone
  • Leena Salmela
  • Alexander Schönhuth
  • Marinella Sciortino
  • Jouni Sirén
  • Jens Stoye
  • Tomáš Vinař