TOGGLE

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Toolbox for generic NGS analyses - A framework to quickly build pipelines and to perform large-scale NGS analysis

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TOGGLE : Toolbox for generic NGS analyses
===========

![TOGGLE Logo](https://raw.githubusercontent.com/SouthGreenPlatform/TOGGLE/master/images/toggleLogo.png)

Dear Biologist, have you ever dreamed of using the whole power of those numerous NGS tools that your bioinformatician colleagues use through this awful list of command line ?

Dear Bioinformatician, have you ever guess how to design really fastly a new NGS pipeline without having to retype again dozens of code lines to readapt your scripts or starting from scratch ?

**So, be Happy ! TOGGLE is for you !!**

TOGGLE (TOolbox for Generic nGs anaLysEs) is a suite of 19 packages and more than 110 modules able to manage a large set of NGS softwares
and utilities to easily design pipelines able to handle hundreds of samples. 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, that can be changed for each assay without
having to change the code itself.

[More information on our website](http://toggle.southgreen.fr)

* [Follow the installation instructions](http://toggle.southgreen.fr/install/install/)
* [You can find a detailed Manual here](http://toggle.southgreen.fr/manual/quickManual/)
* [You can find detailed known issues](http://toggle.southgreen.fr/FAQ/knownIssues/)
* [Current Release Notes](http://toggle.southgreen.fr/install/releaseNotes/)
* [Development version](#development-version)
* [Contributing](#contributing)
* [Contact](#contact)
* [Citation](#citation)

## Development version
You are currently on the production version, *i.e.* the last stable one. A more advanced version, the dev version is available on the [TOGGLE-DEV gitHub](https://github.com/SouthGreenPlatform/TOGGLE-DEV)

##  Contributing

* Licencied under CeCill-C (http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html) and GPLv3
* Intellectual property belongs to IRD, CIRAD, ADNid and SouthGreen development platform
* Written by Christine Tranchant-Dubreuil, Sebastien Ravel, Maryline Summo, Cédric Farcy, Enrique Ortega-Abboud, Mawussé Agbessi, Cecile Monat, Ayité Kougbeadjo, Souhila Amanzougarene, Gautier Sarah, Abdoulaye Diallo, Laura Helou, Alexis Dereeper, Ndomassi Tando, Julie Orjuela-Bouniol, and Francois Sabot
* Copyright 2014-2018

## Contact

For bug tracking purpose you can use the GitHub or questions about TOGGLE, you can contact the developers at
[toggle@ird.fr](mailto:toggle@ird.fr)

##  Citation
**TOGGLe, a flexible framework for easily building complex workflows and performing robust large-scale NGS analyses**
Christine Tranchant-Dubreuil, Sebastien Ravel, Cecile Monat, Gautier Sarah, Abdoulaye Diallo, Laura Helou, Alexis Dereeper, Ndomassi Tando, Julie Orjuela-Bouniol, Francois Sabot.
*bioRxiv*, doi: https://doi.org/10.1101/245480
https://toggle.southgreen.fr/

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