Introduction

MOTIVATION: Efficient and fast next-generation sequencing (NGS) algorithms are essential to analyze the terabytes of data generated by the NGS machines. A serious bottleneck can be the design of such algorithms, as they require sophisticated data structures and advanced hardware implementation. RESULTS: We propose an open-source library dedicated to genome assembly and analysis to fasten the process of developing efficient software. The library is based on a recent optimized de-Bruijn graph implementation allowing complex genomes to be processed on desktop computers using fast algorithms with low memory footprints. AVAILABILITY AND IMPLEMENTATION: The GATB library is written in C++ and is available at the following Web site http://gatb.inria.fr under the A-GPL license. CONTACT: lavenier@irisa.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publications

  1. GATB: Genome Assembly & Analysis Tool Box.
    Cite this
    Drezen E, Rizk G, Chikhi R, Deltel C, Lemaitre C, Peterlongo P, Lavenier D, 2014-10-01 - Bioinformatics (Oxford, England)

Credits

  1. Erwan Drezen
    Developer

    INRIA/IRISA/GenScale, Campus de Beaulieu, United States of America

  2. Guillaume Rizk
    Developer

    INRIA/IRISA/GenScale, Campus de Beaulieu, United States of America

  3. Rayan Chikhi
    Developer

    INRIA/IRISA/GenScale, Campus de Beaulieu, United States of America

  4. Charles Deltel
    Developer

    INRIA/IRISA/GenScale, Campus de Beaulieu, United States of America

  5. Claire Lemaitre
    Developer

    INRIA/IRISA/GenScale, Campus de Beaulieu, United States of America

  6. Pierre Peterlongo
    Developer

    INRIA/IRISA/GenScale, Campus de Beaulieu, United States of America

  7. Dominique Lavenier
    Investigator

    INRIA/IRISA/GenScale, Campus de Beaulieu, United States of America

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Summary
AccessionBT006326
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByDominique Lavenier