title: 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).
  
  
  CONCLUSIONS
  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. The whole code and test data are available at https://github.com/SouthGreenPlatform/TOGGLE .
authors.affiliation: UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. cecile.monat@ird.fr.
authors.forename: Cécile
authors.initials: C
authors.lastname: Monat
authors.affiliation: UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. christine.tranchant@ird.fr.
authors.forename: Christine
authors.initials: C
authors.lastname: Tranchant-Dubreuil
authors.affiliation: UMR AGAP CIRAD/INRA/SupAgro, TA A-108/03 - Avenue Agropolis, Montpellier Cedex 5, F-34398, France. ayite.kougbeadjo@cirad.fr.
authors.forename: Ayité
authors.initials: A
authors.lastname: Kougbeadjo
authors.affiliation: UMR AGAP CIRAD/INRA/SupAgro, TA A-108/03 - Avenue Agropolis, Montpellier Cedex 5, F-34398, France. cedric.farcy@cirad.fr.
authors.forename: Cédric
authors.initials: C
authors.lastname: Farcy
authors.affiliation: UMR AGAP CIRAD/INRA/SupAgro, TA A-108/03 - Avenue Agropolis, Montpellier Cedex 5, F-34398, France. enrique.ortega-abboud@cirad.fr.
authors.forename: Enrique
authors.initials: E
authors.lastname: Ortega-Abboud
authors.affiliation: UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. souhila.amanzougarene@ird.fr.
authors.forename: Souhila
authors.initials: S
authors.lastname: Amanzougarene
authors.affiliation: UMR-BGPI CIRAD TA A-54/K, Campus International de Baillarguet, Montpellier Cedex 5, F-34398, France. sebastien.ravel@cirad.fr.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Ravel
authors.affiliation: UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. mawusse.agbessi@ird.fr.
authors.forename: Mawussé
authors.initials: M
authors.lastname: Agbessi
authors.affiliation: ADNid, Cap Alpha, Avenue de l'Europe, Clapiers, F-34830, France. julie.orjuela@adnid.fr.
authors.forename: Julie
authors.initials: J
authors.lastname: Orjuela-Bouniol
authors.affiliation: UMR AGAP CIRAD/INRA/SupAgro, TA A-108/03 - Avenue Agropolis, Montpellier Cedex 5, F-34398, France. maryline.summo@cirad.fr.
authors.forename: Maryline
authors.initials: M
authors.lastname: Summo
authors.affiliation: UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. francois.sabot@ird.fr.
authors.forename: François
authors.initials: F
authors.lastname: Sabot
mesh_terms: D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012984:Software; D059467:Transcriptome