Publications des scientifiques de l'IRD

Monat Cécile, Dubreuil Tranchant Christine, Kougbeadjo A., Farcy C., Ortega-Abboud E., Amanzougarene S., Ravel S., Agbessi M., Orjuela-Bouniol J., Summo M., Sabot François. (2015). TOGGLE : toolbox for generic NGS analyses. Bmc Bioinformatics, 16, art. 374 [8 p.]. ISSN 1471-2105.

Titre du document
TOGGLE : toolbox for generic NGS analyses
Année de publication
2015
Type de document
Article référencé dans le Web of Science WOS:000364458100001
Auteurs
Monat Cécile, Dubreuil Tranchant Christine, Kougbeadjo A., Farcy C., Ortega-Abboud E., Amanzougarene S., Ravel S., Agbessi M., Orjuela-Bouniol J., Summo M., Sabot François
Source
Bmc Bioinformatics, 2015, 16, art. 374 [8 p.] ISSN 1471-2105
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.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020] ; Informatique [122]
Localisation
Fonds IRD [F B010065444]
Identifiant IRD
fdi:010065444
Contact