GenScale

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, …