Section: Partnerships and Cooperations

International Initiatives

• Title: High-Performance Combinatorial Optimization for Computational Genomics

• International Partner (Institution - Laboratory - Researcher):

  • Los Alamos National Laboratory (LANL)-NM, United States, CCS-3, Hristo Djidjev

• Start year: 2017

• Teams' web site:  https://team.inria.fr/genscale/presentation/associated-team/

Genome sequencing and assembly, the determination of the DNA sequences of a genome, is a core experiment in computational biology. During the last decade, the cost of sequencing has decreased dramatically and a huge amount of new genomes have been sequenced. Nevertheless, most of recent genome projects stay unfinished and nowadays the databases contain much more incompletely assembled genomes than whole stable reference genomes. The main reason is that producing a complete genome, or an as-complete-as-possible-genome, is an extremely difficult computational task (an NP-hard problem) and, in spite of the efforts and the progress done by the bioinformatics community, no satisfactory solution is available today. New sequencing technologies (such as PacBio or Oxford Nanopore) are being developed that tend to produce longer DNA sequences and offer new opportunities, but also bring significant new challenges. The goal of this joint project–a cooperation between Los Alamos National Laboratory, US and Inria, is to develop a new methodology and tools based on novel optimization techniques and massive parallelism suited to these emerging technologies and able to tackle the complete assembly of large genomes.

• Free University of Brussels, Belgium: Genome assembly [P. Perterlongo, A. Limasset]