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Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

hal.structure.identifierService Expérimentation et Développement [SED [Rennes]]
hal.structure.identifierPlateforme bioinformatique GenOuest [Rennes]
dc.contributor.authorLE BRAS, Yvan
hal.structure.identifierPlateforme bioinformatique GenOuest [Rennes]
hal.structure.identifierService Expérimentation et Développement [SED [Rennes]]
dc.contributor.authorCOLLIN, Olivier
hal.structure.identifierPlateforme bioinformatique GenOuest [Rennes]
hal.structure.identifierService Expérimentation et Développement [SED [Rennes]]
dc.contributor.authorMONJEAUD, Cyril
hal.structure.identifierBaobab [LBBE]
hal.structure.identifierEquipe de recherche européenne en algorithmique et biologie formelle et expérimentale [ERABLE]
dc.contributor.authorLACROIX, Vincent
hal.structure.identifierInstitut de Biologie Computationnelle [IBC]
hal.structure.identifierMéthodes et Algorithmes pour la Bioinformatique [MAB]
dc.contributor.authorRIVALS, Eric
hal.structure.identifierScalable, Optimized and Parallel Algorithms for Genomics [GenScale]
dc.contributor.authorLEMAITRE, Claire
hal.structure.identifierLaboratoire de Biométrie et Biologie Evolutive - UMR 5558 [LBBE]
dc.contributor.authorMIELE, Vincent
hal.structure.identifierBaobab [LBBE]
hal.structure.identifierEquipe de recherche européenne en algorithmique et biologie formelle et expérimentale [ERABLE]
dc.contributor.authorSACOMOTO, Gustavo
hal.structure.identifierBaobab [LBBE]
dc.contributor.authorMARCHET, Camille
hal.structure.identifierInstitut de Biologie Computationnelle [IBC]
hal.structure.identifierMéthodes et Algorithmes pour la Bioinformatique [MAB]
dc.contributor.authorCAZAUX, Bastien
hal.structure.identifierMéthodes et Algorithmes pour la Bioinformatique [MAB]
dc.contributor.authorEL AABIDINE, Amal Zine
hal.structure.identifierHelsinki Institute for Information Technology [HIIT]
dc.contributor.authorSALMELA, Leena
hal.structure.identifierScalable, Optimized and Parallel Algorithms for Genomics [GenScale]
dc.contributor.authorALVES CARVALHO, Susete
hal.structure.identifierScalable, Optimized and Parallel Algorithms for Genomics [GenScale]
dc.contributor.authorANDRIEUX, Alexan
hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
hal.structure.identifierCentre de Bioinformatique de Bordeaux [CBIB]
dc.contributor.authorURICARU, Raluca
hal.structure.identifierScalable, Optimized and Parallel Algorithms for Genomics [GenScale]
dc.contributor.authorPETERLONGO, Pierre
dc.date.accessioned2024-04-15T09:57:00Z
dc.date.available2024-04-15T09:57:00Z
dc.date.issued2016-02
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/198881
dc.description.abstractEnBackground: 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 computingresources, and potentially removing or modifying parts of the biological information contained in the data. Ourapproach proposes to focus directly on biological questions, by considering raw unassembled NGS data, through asuite of six command-line tools.Findings: Dedicated to ‘whole-genome assembly-free’ treatments, the Colib’read tools suite uses optimizedalgorithms for various analyses of NGS datasets, such as variant calling or read set comparisons. Based on the use of ade 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. Tofacilitate 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 NGSdata. More importantly, our approach allows the maximum biological information to be retained in the data, and usesa very low memory footprint.
dc.description.sponsorshipDigital and Hardware Solutions and Modeling for the Environement and Life Sciences
dc.language.isoen
dc.publisherOxford Univ Press
dc.subject.enMetagenomics
dc.subject.enDe Bruijn graph
dc.subject.enWhole-genome assembly-less treatment
dc.subject.enBloom filter
dc.subject.enNGS
dc.subject.enRNA-seq
dc.subject.enVariant calling
dc.subject.enlong read correction
dc.title.enColib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads
dc.typeArticle de revue
dc.identifier.doi10.1186/s13742-015-0105-2
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
bordeaux.journalGigaScience
bordeaux.volume5
bordeaux.hal.laboratoriesLaboratoire Bordelais de Recherche en Informatique (LaBRI) - UMR 5800*
bordeaux.issue1
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionBordeaux INP
bordeaux.institutionCNRS
bordeaux.peerReviewedoui
hal.identifierhal-01280238
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01280238v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=GigaScience&rft.date=2016-02&rft.volume=5&rft.issue=1&rft.au=LE%20BRAS,%20Yvan&COLLIN,%20Olivier&MONJEAUD,%20Cyril&LACROIX,%20Vincent&RIVALS,%20Eric&rft.genre=article


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