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
- Optimized (time and memory) tools dedicated to NGS processing
- Data compression, genome assembly, variant detection, metagenomics, GWAS (genome-wide association Study)
- 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/
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 …
Through the INRIA Associate Team Program, GenScale and Los Alamos National Laboratory, New Mexico, USA, join their effort on the following research project:
High-Performance Combinatorial Optimization for Computational Genomics
Description of the research program
A preprint for our minimal perfect hash library BBHash (formerly BooPHF) is up on arxiv ( ).
Développée par l’équipe de recherche GenScale, au centre Inria Rennes – Bretagne Atlantique, GATB est une boîte à outils pour l’analyse des données issues des séquenceurs génomiques de nouvelle génération. Elle comprend aujourd’hui une douzaine de logiciels spécialisés dans différentes tâches de bio-informatique. Les chercheurs prévoient d’y intégrer une nouvelle application destinée à faciliter le diagnostic pour le traitement des cancers dans les hôpitaux.
A new release (1.0.1) of the RConnector tool (connecting reads from large datasets) is available here.
- Are you interested in learning how to make high-performance software tools to decypher reads data?
- Are you a little familiar with C++ programming?
- Are you happy to come to Spain during Spring 2017?
Ok, this event if fully made for you:
The Genscale team will hold a GATB Special Session during the 5th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2017).
What: tutorial session program is available here (see SS3 session)
When: April 26-27, 2017.
Where: Granada, Spain.
To attend to this third GATB Programming Special Session, you have to register to the IWBBIO conference, here.
In addition, fill in this very short form so that we know you will attend to the GATB Special Session; this is important for us to setup the session appropriately, given the number of attendees.
You may find all slides from the colib’read workshop on the program page.
We propose a PhD subject about read assembly and haplotyping. See dedicated page