Team presentation

GenScale is a bioinformatics research team. It focuses on methodological research at the interface between computer science and genomic. The main objective of the group is the design of scalable, optimized and parallel algorithms for processing the huge amount of genomic data generated by the recent advances of biotechnologies.

GenScale research activities cover the following domains:

  • Next and third generation Sequencing (NGS & TGS)
    • Fast and low memory footprint assembly & Scaffolding
    • Variant extraction on raw data (without assembly)
    • Mapping
  • High throughput sequence analysis
    • Bank to bank comparison
    • de novo comparative Metagenomics
    • 3D Protein structures
      • Comparison, classification
      • Conformation extraction from NMR data
    • Bioinformatics workflows
      • Graphical capture
      • Parallel processing (cluster, cloud)

This pure computer science activity is maintained with strong collaboration with life science research groups on challenging genomic projects.

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

NEW minimal perfect hash library BBHASH

A preprint for our minimal perfect hash library BBHash (formerly BooPHF) is up on arxiv ( ).

 

Un outil d’analyse génomique pour le diagnostic cancer

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.

La suite…

New Short Read Connector Release

A new release (1.0.1) of the RConnector tool (connecting reads from large datasets) is available here.

GATB Programming Day – Spring 2017

  • 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.

Slides from the colib’read workshop available

You may find all slides from the colib’read workshop on the program page.

Phd subject proposal

We propose a PhD subject about read assembly and haplotyping. See dedicated page

Workshop Colib’Read – Program Online

Hi all,

The Colib’read workshop program is now online on this page http://gdr-bim.cnrs.fr/colibread/program/.

We remind you that the attendance is free but ***registration is mandatory*** see website: http://gdr-bim.cnrs.fr/colibread/.
Note that space is limited, and registration will be taken in the order received.

— WHAT —
Calling biological information from raw reads and long reads correction. All methods are reference free.

— HOW —
The workshop is composed of overview and practical talks, of success stories (bioanalyses results), of tools demonstrations and of interactive discussions.

— WHEN —
November 7,8 2016

— LANGUAGE —
English

— WHERE —
Institut Curie – Amphithéâtre Constant Burg  12, Rue Lhomond 75005 Pari

— REGISTRATION —
The workshop attendance is free but ***registration is mandatory*** (see website)

— WEB SITE —
http://gdr-bim.cnrs.fr/colibread/

Short Read Connector presentation

Short Read Connector was published and presented during the Prague Stringology Conference 2016.

Slides available from Pierre’s presentation page.

Simka presentation

Simka (de novo metagenomics comparisons) was presented during the “Pasteur Metagenomics Summer School“.

Check the Pierre’s presentation page.

GATB programming day – Fall 2016

Are you interested in learning how to create high-performance NGS data analysis tools?
Are you familiar with C++ programming and can you speak English?

If so, Ok, well done ;). This event is for you:

The GATB programming day: learn the basics of high-performance NGS data processing using the GATB-Corelibrary.

This second edition of our GATB Tutorial is scheduled on November, 9th 2016 in Paris, France.

Details of the tutorial session is available here.