TOGGLE: toolbox for generic NGS analyses

BMC Bioinformatics

Software

Julie Orjuela-Bouniol¹  Enrique Ortega-Abboud²  Maryline Summo²  Ayité Kougbeadjo²  Cédric Farcy²  Christine Tranchant-Dubreuil³  François Sabot³  Cécile Monat³  Souhila Amanzougarene³  Mawussé Agbessi³  Sébastien Ravel⁴ 

[1] ADNid, Cap Alpha, Avenue de l’Europe, F-34830, Clapiers, France;UMR AGAP CIRAD/INRA/SupAgro, TA A-108/03 - Avenue Agropolis, F-34398, Montpellier Cedex 5, France;UMR DIADE IRD/UM, 911 Avenue Agropolis, F-34934, Montpellier Cedex 5, France;UMR-BGPI CIRAD TA A-54/K, Campus International de Baillarguet, F-34398, Montpellier Cedex 5, France;

关键词: NGS;    Toolbox;    Pipeline;    Flexible;   

DOI  :  10.1186/s12859-015-0795-6

 received in 2015-05-14, accepted in 2015-10-24,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsTOGGLE (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).ConclusionTOGGLE 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.

【 授权许可】

Unknown   
© Monat et al.; licensee BioMed Central. 2015. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.