TOGGLE pipeline

TOGGLE specifications


Unique identifier OMICS_10558
Alternative name TOolbox for Generic nGs anaLysEs
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages Perl
License CeCILL version 2.1
Computer skills Advanced
Version 0.3.5
Stability Stable
Requirements Java, bwa, SAMtools, CutAdapt, FastqC, PicardTools, GATK, Perl:: Data::Dumper, Data::Translate, Test:More, Test::Deep, Capture::Tiny
Maintained Yes


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  • person_outline Francois Sabot <>
  • person_outline Christine Tranchant-Dubreuil <>

Publications for TOolbox for Generic nGs anaLysEs


TOGGLe, a flexible framework for easily building complex workflows and performing robust large-scale NGS analyses.

2018 BioRxiv
DOI: 10.1101/245480

TOGGLE: toolbox for generic NGS analyses.

2015 BMC Bioinformatics
PMCID: 4640241
PMID: 26552596
DOI: 10.1186/s12859-015-0795-6
TOGGLE institution(s)
DIADE IRD, University of Montpellier, Montpellier, France; BGPI CIRAD, INRA, TA A-54/K, Campus International de Baillarguet, Montpellier, France; AGAP CIRAD, INRA, SupAgro, TA A-108/03, Montpellier, France; ADNid-QualTech, Montferrier-sur-Lez, France; IPME IRD, University of Montpellier, Montpellier, France; South Green Bioinformatics Platform, BIOVERSITY, CIRAD, INRA, IRD, SupAgro, Montpellier, France
TOGGLE funding source(s)
Supported by grants from ANR (AfriCrop project #ANR-13-BSV7-0017) and NUMEV Labex (LandPanToggle #2015-1-030-LARMANDE).

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