title: Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads.
abstract: BACKGROUND
  With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of computing resources, and potentially removing or modifying parts of the biological information contained in the data. Our approach proposes to focus directly on biological questions, by considering raw unassembled NGS data, through a suite of six command-line tools.
  
  
  RESULTS
  Dedicated to 'whole-genome assembly-free' treatments, the Colib'read tools suite uses optimized algorithms for various analyses of NGS datasets, such as variant calling or read set comparisons. Based on the use of a de Bruijn graph and bloom filter, such analyses can be performed in a few hours, using small amounts of memory. Applications using real data demonstrate the good accuracy of these tools compared to classical approaches. To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories.
  
  
  CONCLUSIONS
  With the Colib'read Galaxy tools suite, we enable a broad range of life scientists to analyze raw NGS data. More importantly, our approach allows the maximum biological information to be retained in the data, and uses a very low memory footprint.
authors: GenOuest Core Facility, UMR6074 IRISA CNRS/INRIA/Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex France.
authors: Yvan
authors: Y
authors: Le Bras
authors: GenOuest Core Facility, UMR6074 IRISA CNRS/INRIA/Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex France.
authors: Olivier
authors: O
authors: Collin
authors: GenOuest Core Facility, UMR6074 IRISA CNRS/INRIA/Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex France.
authors: Cyril
authors: C
authors: Monjeaud
authors: BAMBOO team, INRIA Grenoble Rhône-Alpes & Laboratoire Biométrie et Biologie Évolutive, UMR5558 CNRS, Université Claude Bernard (Lyon 1), Campus de la Doua, 43 Boulevard du 11 Novembre 1918, Villeurbanne Cedex, 69622 France.
authors: Vincent
authors: V
authors: Lacroix
authors: MAB team, UMR5506 CNRS, Université Montpellier II, Sciences et techniques, Université Montpellier 2 LIRMM UMR 5506 CC477 161 rue Ada, Montpellier, 34095 Cedex 5 France.
authors: Éric
authors: É
authors: Rivals
authors: INRIA/IRISA, Genscale team, UMR6074 IRISA CNRS/INRIA/Université de Rennes 1, Campus de Beaulieu, Rennes, 35042 Cedex France.
authors: Claire
authors: C
authors: Lemaitre
authors: BAMBOO team, INRIA Grenoble Rhône-Alpes & Laboratoire Biométrie et Biologie Évolutive, UMR5558 CNRS, Université Claude Bernard (Lyon 1), Campus de la Doua, 43 Boulevard du 11 Novembre 1918, Villeurbanne Cedex, 69622 France.
authors: Vincent
authors: V
authors: Miele
authors: BAMBOO team, INRIA Grenoble Rhône-Alpes & Laboratoire Biométrie et Biologie Évolutive, UMR5558 CNRS, Université Claude Bernard (Lyon 1), Campus de la Doua, 43 Boulevard du 11 Novembre 1918, Villeurbanne Cedex, 69622 France.
authors: Gustavo
authors: G
authors: Sacomoto
authors: BAMBOO team, INRIA Grenoble Rhône-Alpes & Laboratoire Biométrie et Biologie Évolutive, UMR5558 CNRS, Université Claude Bernard (Lyon 1), Campus de la Doua, 43 Boulevard du 11 Novembre 1918, Villeurbanne Cedex, 69622 France.
authors: Camille
authors: C
authors: Marchet
authors: MAB team, UMR5506 CNRS, Université Montpellier II, Sciences et techniques, Université Montpellier 2 LIRMM UMR 5506 CC477 161 rue Ada, Montpellier, 34095 Cedex 5 France.
authors: Bastien
authors: B
authors: Cazaux
authors: MAB team, UMR5506 CNRS, Université Montpellier II, Sciences et techniques, Université Montpellier 2 LIRMM UMR 5506 CC477 161 rue Ada, Montpellier, 34095 Cedex 5 France.
authors: Amal
authors: A
authors: Zine El Aabidine
authors: Department of Computer Science and Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, FI-00014 Finland.
authors: Leena
authors: L
authors: Salmela
authors: INRIA/IRISA, Genscale team, UMR6074 IRISA CNRS/INRIA/Université de Rennes 1, Campus de Beaulieu, Rennes, 35042 Cedex France.
authors: Susete
authors: S
authors: Alves-Carvalho
authors: INRIA/IRISA, Genscale team, UMR6074 IRISA CNRS/INRIA/Université de Rennes 1, Campus de Beaulieu, Rennes, 35042 Cedex France.
authors: Alexan
authors: A
authors: Andrieux
authors: University of Bordeaux, LaBRI/CNRS, Talence, F-33405 France ; University of Bordeaux, CBiB, Bordeaux, F-33000 France.
authors: Raluca
authors: R
authors: Uricaru
authors: INRIA/IRISA, Genscale team, UMR6074 IRISA CNRS/INRIA/Université de Rennes 1, Campus de Beaulieu, Rennes, 35042 Cedex France.
authors: Pierre
authors: P
authors: Peterlongo
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D016678:Genome / Q000235:genetics; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D008969:Molecular Sequence Data; D015203:Reproducibility of Results; D012984:Software
keywords: Bloom filter; De Bruijn graph; Metagenomics; NGS; RNA-seq; Variant calling; Whole-genome assembly-less treatment; long read correction