TOGGLE : Toolbox for generic NGS analyses

TOGGLE (TOolbox for Generic nGs anaLysEs) is a suite of 10 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.

We present also the implementation of TOGGLE in a complete analysis pipeline designed for SNP discovery for large sets of NGS data, ready to use in different environments (single machine to HPC clusters).

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 Cecile Monat, Christine Tranchant, Ayite Kougbeadjo, Cedric Farcy, Mawusse Agbessi, Enrique Ortega-Abboud, Sébastien Ravel, Julie Orjuela-Bouniol, Souhila Amanzougarene, Gauthier Sarah, Marilyne Summo, and Francois Sabot
• Copyright 2014-2015

Contact

For bug tracking purpose you can use the GitHub or questions about TOGGLE, you can contact the mainteners using the following email addresses:

• christine.tranchant_at_ird.fr
• francois.sabot_at_ird.fr

Citation

TOGGLE: Toolbox for generic NGS analyses. Cécile Monat, Christine Tranchant-Dubreuil, Ayité Kougbeadjo, Cédric Farcy, Enrique Ortega-Abboud, Souhila Amanzougarene, Sébastien Ravel, Mawussé Agbessi, Julie Orjuela-Bouniol, Maryline Summo and François Sabot.

BMC Bioinformatics 2015, 16:374 doi:10.1186/s12859-015-0795-6

INSTALLATION

Follow the INSTALLATION instructions

MANUAL

You can find a detailed MANUAL here

Release Notes

Current Release Notes

REQUIREMENTS

Perl

• Data::Translate
• Data::Dumper
• Test::More
• Test::Deep
• Capture::Tiny
• List::Compare
• Switch

Bioinformatics software (minimal version)

• Perl 5.16
• java 1.7
• BWA 0.7.2
• SAMtools 0.1.18
• picardTools 1.63
• gatk 3.3
• fastQC v0.10.1
• cutadapt 1.2.1
• FastxToolkit
• Tophat
• Snpeff

Bioinformatics tools included

#####BWA (http://bio-bwa.sourceforge.net/)

• bwaAln
• bwaSampe
• bwaSamse
• bwaIndex
• bwaMem

#####SamTools (http://samtools.sourceforge.net/)

• samToolsFaidx
• samToolsIndex
• samToolsView
• samToolsSort
• mergeHeader
• samToolsMerge
• samToolsIdxstats
• samToolsDepth
• samToolsFlagstat

#####PicardTools (http://broadinstitute.github.io/picard/)

• picardToolsMarkDuplicates
• picardToolsCreateSequenceDictionary
• picardToolsSortSam
• picardToolsAddOrReplaceReadGroup
• picardToolsValidateSamFile
• picardToolsCleanSam
• picardToolsSamFormatConverter

#####Gatk (https://www.broadinstitute.org/gatk/)

• gatkBaseRecalibrator
• gatkRealignerTargetCreator
• gatkIndelRealigner
• gatkHaplotypeCaller
• gatkSelectVariants
• gatkVariantFiltration
• gatkReadBackedPhasing
• gatkUnifiedGenotyper
• gatkBaseRecalibrator
• gatkPrintReads

#####Fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

• fastqc

#####FastxToolkit (http://hannonlab.cshl.edu/fastx_toolkit/)

• fastxTrimmer

#####Tophat (https://ccb.jhu.edu/software/tophat/index.shtml)

• bowtiebuild
• bowtie2build
• tophat2

#####Snpeff (http://snpeff.sourceforge.net/)

• snpeffAnnotation

#####Cutadapt (https://pypi.python.org/pypi/cutadapt)

• cutadapt

OPTIONAL

• Graphviz v2.xx (http://www.graphviz.org/)