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TOGGLE: toolbox for generic NGS analyses

Monat Cécile, Tranchant-Dubreuil Christine, Kougbeadjo Ayite, Farcy Cédric, Ortega-Abboud Enrique, Amanzougarene Souhila, Ravel Sébastien, Agbessi Mawussé, Orjuela-Bouniol Julie, Summo Marilyne, Sabot François. 2015. TOGGLE: toolbox for generic NGS analyses. BMC Bioinformatics, 16 (374) : 1-8.

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Jeu de données : https://github.com/SouthGreenPlatform/TOGGLE

Quartile : Q1, Sujet : MATHEMATICAL & COMPUTATIONAL BIOLOGY / Quartile : Q2, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q3, Sujet : BIOCHEMICAL RESEARCH METHODS

Résumé : Background: The explosion of NGS (Next Generation Sequencing) sequence data requires a huge effort in Bioinformatics methods and analyses. The creation of dedicated, robust and reliable pipelines able to handle dozens of samples from raw FASTQ data to relevant biological data is a time-consuming task in all projects relying on NGS. To address this, we created a generic and modular toolbox for developing such pipelines. Results: TOGGLE (TOolbox for Generic nGs anaLysEs) is a suite of tools able to design pipelines that manage large sets of NGS softwares and utilities. Moreover, TOGGLE offers an easy way to manipulate the various options of the different softwares through the pipelines in using a single basic configuration file, which can be changed for each assay without having to change the code itself. We also describe one implementation of TOGGLE in a complete analysis pipeline designed for SNP discovery for large sets of genomic data, ready to use in different environments (from a single machine to HPC clusters). Conclusion: TOGGLE speeds up the creation of robust pipelines with reliable log tracking and data flow, for a large range of analyses. Moreover, it enables Biologists to concentrate on the biological relevance of results, and change the experimental conditions easily. The whole code and test data are available at https://github.com/SouthGreenPlatform/TOGGLE. (Résumé d'auteur)

Mots-clés libres : NGS, Toolbox, Pipeline, Flexible

Classification Agris : U10 - Méthodes mathématiques et statistiques
U40 - Méthodes de relevé
F30 - Génétique et amélioration des plantes
L10 - Génétique et amélioration des animaux

Axe stratégique Cirad : Hors axes (2014-2018)

Auteurs et affiliations

  • Monat Cécile, IRD (FRA)
  • Tranchant-Dubreuil Christine, IRD (FRA)
  • Kougbeadjo Ayite, INRA (FRA)
  • Farcy Cédric, CIRAD-BIOS-UMR AGAP (FRA)
  • Ortega-Abboud Enrique, INRA (FRA)
  • Amanzougarene Souhila, IRD (FRA)
  • Ravel Sébastien, CIRAD-BIOS-UMR BGPI (FRA)
  • Agbessi Mawussé, IRD (FRA)
  • Orjuela-Bouniol Julie, CIRAD-BIOS-UMR AGAP (FRA)
  • Summo Marilyne, CIRAD-BIOS-UMR AGAP (FRA)
  • Sabot François, IRD (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/579008/)

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