Paper CARNAC-LR published in NAR: “De novo clustering of long reads by gene from transcriptomics data”

Our paper “De novo clustering of long reads by gene from transcriptomics data” was published late October 2018 in NAR.

It describes the CARNAC-LR tool developed by Camille Marchet

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Long Reads RNA-seq de novo clustering – preprint

De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets



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discoSnp goes to RAD seq

We propose an adaptation of DiscoSnp for RadSeq data.

  • Novelties:
    • Clustering per locus
    • Predictions of variants close to sequence extremities
    • Order(s) of magnitude faster than Stack or IPyRAD.
  • Predictions have high precision (up to 99.3% on simulated data) with good recall (82.2% when using high precision parameters)
  • Applied on real biological data, RAD data from 259 specimens of Chiastocheta flies, morphologically assigned to 7 species, all individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within species structuration and the existence of two populations linked to their geographic distributions.


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International Collaboration : Associate Team with LANL, NM, USA

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

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NEW minimal perfect hash library BBHASH

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


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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…

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New Short Read Connector Release

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

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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.

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Slides from the colib’read workshop available

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

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Phd subject proposal

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

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