TOGGLE-3 : a tool for on the fly pipelines creation and performing robust large-scale NGS analyses

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Submitted on 2 Jun 2020

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TOGGLE-3 : a tool for on the fly pipelines creation and

performing robust large-scale NGS analyses

Sébastien Ravel, Christine Tranchan-Dubreuil, Cécile Monat, Gautier Sarah,

Julie Orjuela-Bouniol, Francois Sabot

To cite this version:

Sébastien Ravel, Christine Tranchan-Dubreuil, Cécile Monat, Gautier Sarah, Julie Orjuela-Bouniol, et al.. TOGGLE-3 : a tool for on the fly pipelines creation and performing robust large-scale NGS analyses. JOBIM 2016 : Journées ouvertes de biologie informatique et mathématiques, Jun 2016, Lyon, France. 437 p., 2016, JOBIM 2016. �hal-02738889�

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Sébastien Ravel et al.

TOGGLE-3 : a tool for on the fly pipelines

creation and performing robust large-scale NGS

analyses

Poster 27

_{Sébastien Ravel}

* †1

_{, Christine Tranchan-Dubreuil}

‡2

_{, Cécile Monat}

2

_,

Gautier Sarah

3

, Julie Orjuela-Bouniol

4

, François Sabot

§2

1_{Biologie et génétique des interactions plantes-parasites pour la protection intégrée (BGPI) – Institut}

national de la recherche agronomique (INRA) : UR0385, Centre de coopération internationale en recherche agronomique pour le développement [CIRAD] : UMR54 –

Campus International de Baillarguet - TA 41 / K, F-34 398 M Cedex 05, France

2_{Diversité, adaptation, développement des plantes (DIADE) – Institut de recherche pour le}

développement [IRD] : UR232, Université Montpellier II - Sciences et techniques – Centre IRD de Montpellier 911 av Agropolis BP 604501, F-34 394 M Cedex 5, France

3_{Amélioration Génétique et Adaptation des Plantes Méditerranéeennes et Tropicales (AGAP) –}

Montpellier SupAgro, Institut national de la recherche agronomique (INRA) : UMR1334, CIRAD-BIOS – TA A-108/03 Avenue Agropolis, F-34 398 M Cedex 5, France

4_{ADNid company – 830 avenue du Campus Agropolis Baillarguet, F-34 980 M  L, France}

Web site:

https://github.com/SouthGreenPlatform/TOGGLE

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 lines ?

Dear bioinformatician, have you ever wished for a really quick way of designing 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 !

With TOGGLE (TOolbox for Generic nGs anaLysEs), you can create your own pipeline through an easy and user-friendly approach. Indeed, TOGGLE integrate a large set of NGS softwares and utilities to easily design pipelines able to handle hundreds of samples. The pipelines can start from Fastq (plain or compressed), SAM, BAM or VCF (plain or compressed) files, with parallel (by sample) and global analyses (by multi samples).

Moreover, TOGGLE offers an easy way to configure your pipeline with a single configuration file:

— organizing the different steps of workflow, — setting the parameters for the different softwares,

— managing storage space through compressing/deleting intermediate data,

— determining the way the jobs are managed (serial or parallel jobs through scheduler SGE and SLURM).

TOGGLE can work on your laptop, on a single machine server as well as on a HPC system, as a local instance or in a Docker machine. The only limit will be your available space on the storage system, not the amount of samples to be treated or the number of steps.

*. Intervenant

†. Corresponding author :sebastien.ravel@cirad.fr

‡. Corresponding author :christine.tranchant@ird.fr

§. Corresponding author :francois.sabot@ird.fr 214

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-Sébastien Ravel et al. TOGGLE was used on different organisms, from a single sample to more than one hundred at

a time, in RNAseq, DNAreseq/SNP discovery and GBS analyses. List of bioinformatics tools included:

— BWA : bwaAln, bwaSampe, bwaSamse, bwaIndex, bwaMem

— SamTools : samToolsFaidx, samToolsIndex, samToolsView, samToolsSort, mergeHeader, samToolsMerge, samToolsIdxstats, samToolsDepth, SamToolsFlagstat, samToolsMpileUp — PicardTools : picardToolsMarkDuplicates, picardToolsCreateSequenceDictionary,

pi-cardToolsSortSam, picardToolsAddOrReplaceReadGroup, picardToolsValidateSamFile, picardToolsCleanSam, picardToolsSamFormatConverter

— GATK : gatkBaseRecalibrator, gatkRealignerTargetCreator, gatkIndelRealigner, gatkHap-lotypeCaller, gatkSelectVariants, gatkVariantFiltration, gatkReadBackedPhasing, gatkUni-fiedGenotyper, gatkBaseRecalibrator, gatkPrintReads

— Fastqc : fastqc

— FastxToolkit : fastxTrimmer

— Tophat : bowtie-build, bowtie2-build, tophat2 — Snpeff : snpeffAnnotation

— Cutadapt : cutadapt — Graphviz v2.xx (optional) References

[1] 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

Mots clefs : NGS, Toolbox, On the fly pipeline, Flexible, RNASeq, GBS, SNP, Scheduler