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TOGGLE: toolbox for generic NGS analyses.

Cécile Monat1, Christine Tranchant-Dubreuil2, Ayité Kougbeadjo3

  • 1UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. cecile.monat@ird.fr.

BMC Bioinformatics
|November 11, 2015
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Summary
This summary is machine-generated.

TOGGLE accelerates the development of robust bioinformatics pipelines for Next Generation Sequencing (NGS) data analysis. This toolbox simplifies managing NGS software and enables biologists to focus on biological insights.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Next Generation Sequencing (NGS) generates vast amounts of data, necessitating efficient bioinformatics pipelines.
  • Developing robust and reliable pipelines for NGS data analysis is a significant time investment.
  • Existing methods often require extensive coding for each new project or assay.

Purpose of the Study:

  • To introduce TOGGLE (TOolbox for Generic nGs anaLysEs), a generic and modular toolbox for creating bioinformatics pipelines.
  • To provide a user-friendly solution for managing diverse NGS software and their options.
  • To streamline the process of analyzing large-scale genomic datasets.

Main Methods:

  • TOGGLE is a suite of tools designed for building adaptable bioinformatics pipelines.
  • It utilizes a single configuration file to manage software options, allowing easy modification for different assays.
  • The toolbox supports various computing environments, from single machines to High-Performance Computing (HPC) clusters.

Main Results:

  • TOGGLE significantly speeds up the creation of robust analysis pipelines with reliable logging and data flow.
  • An implementation of TOGGLE for SNP discovery in large genomic datasets is presented.
  • The developed pipeline is ready for deployment in diverse computational environments.

Conclusions:

  • TOGGLE facilitates the rapid development of versatile and dependable bioinformatics pipelines for various analyses.
  • It empowers biologists to concentrate on interpreting biological results rather than pipeline development.
  • The toolbox allows for easy adaptation to changing experimental conditions and requirements.