LE BRAS, Yvan; COLLIN, Olivier; MONJEAUD, Cyril; LACROIX, Vincent; RIVALS, Eric; LEMAITRE, Claire; MIELE, Vincent; SACOMOTO, Gustavo; MARCHET, Camille; CAZAUX, Bastien; EL AABIDINE, Amal Zine; SALMELA, Leena; ALVES CARVALHO, Susete; ANDRIEUX, Alexan; URICARU, Raluca; PETERLONGO, Pierre

doi:10.1186/s13742-015-0105-2

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LE BRAS, Yvan
Service Expérimentation et Développement [SED [Rennes]]
Plateforme bioinformatique GenOuest [Rennes]

COLLIN, Olivier
Plateforme bioinformatique GenOuest [Rennes]
Service Expérimentation et Développement [SED [Rennes]]

MONJEAUD, Cyril
Plateforme bioinformatique GenOuest [Rennes]
Service Expérimentation et Développement [SED [Rennes]]

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Article de revue

Ce document a été publié dans

GigaScience. 2016-02, vol. 5, n° 1

Oxford Univ Press

Résumé en anglais

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 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.< Réduire

Mots clés en anglais

Metagenomics

De Bruijn graph

Whole-genome assembly-less treatment

Bloom filter

NGS

RNA-seq

Variant calling

long read correction

URI

https://oskar-bordeaux.fr/handle/20.500.12278/198881

DOI

http://dx.doi.org/10.1186/s13742-015-0105-2

Project ANR

Digital and Hardware Solutions and Modeling for the Environement and Life Sciences - ANR-10-LABX-0020

Origine

Importé de hal

Unités de recherche

Laboratoire Bordelais de Recherche en Informatique (LaBRI) - UMR 5800