Team presentation

GenScale is a bioinformatics research team. Its main goal is to develop scalable methods, tools, and software for

processing genomic data. Our research is motivated by the fast development of next-generation sequencing (NGS) and third generation (TGS) technologies that provide very challenging problems both in terms of bioinformatics and computer sciences.

GenScale research is organized along four main axes:

  • Data structures
    • Indexing the mass of genomic data
    • Focus on the de-Bruijn graph structure.
    • Provide end-user and optimized library
  • Algorithms
    • Optimized (time and memory) tools dedicated to NGS processing
    • Data compression, genome assembly, variant detection, metagenomics, GWAS (genome-wide association Study)
  • Parallelism
    • Combine several levels of parallelism
    • Use existing techniques as multithreading or MapReduce
    • Constrained algorithmic development, in particular, targeting hardware accelerators
  • Applications
    • Participate in biology-oriented projects
    • Inra, CEA, National Museum, Hospitals, …

 

Former and recent research domains included 3D protein structure and Bioinformatics workflows.

Permanent link to this article: https://team.inria.fr/genscale/

Associated team

HipcoGen Period of activity : 1 st year of activity Principal investigator (Inria): Rumen Andonov, GenScale/Inria Principal investigator (partner): Hristo Djidjev, CCS-3/LANL, N M / USA Other participants: INRIA/Genscale : S. François (PhD), C. Marchet (Phd), P. Peterlongo (CR, INRIA), D. Lavenier (DR, CNRS) LANL/ CCS-3 : S. Eidenbenz (senior), G. Chennupati (Postdoc), Robyn Miller …

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