Skip to Main content Skip to Navigation
Journal articles

TOGGLE: toolbox for generic NGS analyses

Abstract : 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.
Keywords : ngs toolbox pipeline
Document type :
Journal articles
Complete list of metadata

Cited literature [18 references]  Display  Hide  Download
Contributor : Migration Prodinra <>
Submitted on : Thursday, May 28, 2020 - 9:37:56 AM
Last modification on : Tuesday, September 7, 2021 - 3:36:42 PM


2015-Monat_BMC Bioinformatics_...
Publisher files allowed on an open archive


Distributed under a Creative Commons Attribution 4.0 International License



Cécile Monat, Christine Tranchant-Dubreuil, Ayite Kougbeadjo, Cédric Farcy, Enrique Ortega-Abboud, et al.. TOGGLE: toolbox for generic NGS analyses. BMC Bioinformatics, BioMed Central, 2015, 16, pp.8. ⟨10.1186/s12859-015-0795-6⟩. ⟨hal-02638152⟩



Record views


Files downloads