Section: Partnerships and Cooperations

National Initiatives

ANR

Project FATINTEGER

Participants : Dominique Lavenier, François Moreews.

Coordinateur: F. Gondret

Duration: 36 months (Mar. 2012 - feb. 2015)

Partners: PEGASE Inra Rennes, CNRS IRISA Rennes, AgroCampus Ouest LMA-IRMAR Rennes

The FatInteger project aims to identify some of the transcriptional key players of animal lipid metabolism plasticity, combining high throughput data with statistical approaches, bioinformatics and phylogenetic. GenScale is involved in the design of the workflow for processing the genomic data.

Project SPECIAPHID: Speciation of pea aphids

Participants : Claire Lemaitre, Anaïs Gouin, Fabrice Legeai.

Coordinator: J-C. Simon (Inra)

Duration: 36 months (Jan. 2012 – Dec 2014)

Partners: IGEPP Inra Rennes, CBGP Inra Montpellier, BF2I Inra Lyon.

The SPECIAPHID project aims to understand the adaptation and speciation of pea aphids by re-sequencing and comparing the genomes of numerous aphid individuals. The role of Genscale is to apply and develop new methods to detect variation between re-sequenced genomes, and in particular complex variants such as structural ones.

Project ADA-SPODO: Genetic variation of Spodoptera Frugiperda

Participants : Claire Lemaitre, Fabrice Legeai, Anaïs Gouin, Dominique Lavenier, Pierre Peterlongo.

Coordinator: E. D’Alençon (Inra, Montpellier)

Duration: 39 months (Oct. 2012 – Dec 2015)

Partners: DGIMI Inra Montpellier, CBGP Inra Montpellier, URGI Inra Versailles, Genscale Inria/IRISA Rennes.

The ADA-SPODO project aims at identifying all sources of genetic variation between two strains of an insect pest: Lepidoptera Spodoptera Frugiperda in order to correlate them with host-plant adaptation and speciation. GenScale’s task is to develop new efficient methods to compare complete genomes along with their postgenomic and regulatory data.

Project COLIB'READ: Advanced algorithms for NGS data

Participants : Pierre Peterlongo, Claire Lemaitre, Dominique Lavenier, Fabrice Legeai, Guillaume Rizk, Chloé Riou.

Coordinator: P. Peterlongo (Inria, GenScale, Rennes)

Duration: 36 months (Mar. 2013 – Feb. 2016)

Partners: LIRMM Montpellier, Bamboo Inria Lyon, Genscale Inria/IRISA Rennes.

The main goal of the Colib’Read project is to design new algorithms dedicated to the extraction of biological knowledge from raw data produced by High Throughput Sequencers (HTS). The project proposes an original way of extracting information from such data. The goal is to avoid the assembly step that often leads to a significant loss of information, or generates chimerical results due to complex heuristics. Instead, the strategy proposes a set of innovative approaches that bypass the assembly phase, and that does not require the availability of a reference genome. https://colibread.inria.fr/

Project GATB: Genome Analysis Tool Box

Participants : Dominique Lavenier, Erwan Drezen, Pierre Peterlongo, Claire Lemaitre, Guillaume Rizk, Charles Deltel.

Coordinator: D. Lavenier (Inria/Irisa, GenScale, Rennes)

Duration: 24 months (Feb. 2013 – Jan. 2015)

Partners: GenScale Inria/IRISA, Rennes – DTI Inria, Rennes.

This project aims to develop algorithms and tools for genome analysis based on an compact data structure having a very low memory footprint allowing end-users to process huge volume of genomic data on a simple desktop computer. The GATB is structured around a C++ library from which many efficient NGS tools can be developed. GATB has been published and used outside Genscale (LIRMM, Inria Bamboo team). http://gatb.inria.fr

Project HydroGen: Metagenomic applied to ocean life study

Participants : Dominique Lavenier, Pierre Peterlongo, Claire Lemaitre, Guillaume Rizk, Gaëtan Benoit.

Coordinator: D. Lavenier (Inria/Irisa, GenScale, Rennes)

Duration: 42 months (Nov. 2014 – Apr. 2018)

Partners: CEA (GenosScope, Evry), INRA (AgroParisTech, Paris – MIG, Jouy-en-Jossas).

The HydroGen project aims to design new statistical and computational tools to measure and analyze biodiversity through comparative metagenomic approaches. The support application is the study of ocean biodiversity based on the analysis of seawater samples available from the Tara Oceans expedition.

PIA: Programme Investissement d’Avenir

RAPSODYN: Optimization of the rapeseed oil content and yield under low nitrogen

Participants : Dominique Lavenier, Claire Lemaitre, Pierre Peterlongo.

Coordinator: N. Nessi (Inra, IGEPP, Rennes)

The objective of the Rapsodyn project is the optimization of the rapeseed oil content and yield under low nitrogen input. GenScale is involved in the bioinformatics work package to elaborate advanced tools dedicated to polymorphism and application to the rapeseed plant.

France Génomique: Bio-informatics and Genomic Analysis

Participants : Laurent Bouri, Dominique Lavenier.

Coordinator: J. Weissenbach (Genoscope, Evry)

France Génomique gathers resources from the main French platforms in genomic and bio-informatics. It offers to the scientific community an access to these resources, a high level of expertise and the possibilities to participate in ambitious national and international projects. The GenScale team is involved in the work package “assembly” to provide expertise and to design new assembly tools for the 3rd generation sequencing.

Programs from research institutions

Inria ADT Mapsembler

Participants : Alexan Andrieux, Dominique Lavenier, Claire Lemaitre, Pierre Peterlongo.

The Mapsembler project aims at finalizing and at distributing the Mapsembler tool. It is funded by Inria ADT call (2012) and coordinated by P. Peterlongo from oct. 2012 to sept. 2014. http://alcovna.genouest.org/mapsembler/

Mastodons CNRS Program SéPhHaDé: Computational Challenge of High Throughput Sequencing and Phenotyping in Life Science

Participants : Dominique Lavenier, Erwan Drezen, Ba Diep Nguyen.

Coordinator: E. Rivals (Lirmm, Montpellier)

Duration: 3 years (2012-2014)

Partners: Lirmm et Inria Montpellier, GenScale IRISA/Inria Rennes, Bamboo LIFL, Lille, INRA Montpellier , ISEM, IPMC Nice, CIRAD Montpellier, LSIS Aix Marseille, Tela Botanica Montpellier, UPMC Banyuls/Mer, CEA Evry, LITIS Rouen

This project deals with the management of huge volume of data generated (1) by the new sequencing technologies (2) by the collection of information for phenotyping living organisms. In 2014, GenScale has developed a methodology to compare metagenomic datasets to protein databanks.