TOGGLe (Toolbox for Generic NGS Analyses) A framework to quickly build pipelines and to perform large-scale HTS analysis

Orjuela Castellanos Julie, Ravel Sébastien, Dereeper Alexis, Tando Ndomassi, Sabot François, Tranchant-Dubreuil Christine. 2018. TOGGLe (Toolbox for Generic NGS Analyses) A framework to quickly build pipelines and to perform large-scale HTS analysis. In : JOBIM 2018 Abstracts. SFBI, GdR BiM, IFB, AMU, INSERM, CNRS. Marseille : SFBI, Résumé, 330-331. Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2018), Marseille, 3 Juillet 2018/6 Juillet 2018.

Résumé : High throughput sequencing (HTS) data analyses are done every day for biologist and bioinformatics in order to give biological sense of their data. These analyses must to be reproducible, robust and efficient. A generic tool TOGGLe (Toolbox for Generic NGS Analyses) was developed to allow running simple and complex pipelines without require any programming skills. This workflow manager is friendly to users and transparent for developers. User only need basic Linux commands and to specify freely their favorite software parameters through a simple text file given. TOGGLe manages, controls, verifies and concatenates every step in your favorite workflow. This workflow manager checks structure and compatibility of steps given in the software parameters file, it builds a workflow and launches it. TOGGLe reports parameters, commands executed, software versions as well as errors if they occur. These informations are kept in logs and reports files. Results are organized in a structured tree of directories. TOGGLe allows compressing or removing intermediate data and it uses scheduler machinery. TOGGLe integrates a large panel of tools for HTS analyses (demultiplexing, cleaning, trimming, calling, assembly, structural variation detection, transcriptomic ...) and post-analysis (haplotype detection, population structure ...). This workflow manager is highly flexible on the data type, working on sequencing raw data (Illumina, 454 or Pacific Biosciences), as well as on various other formats (e.g. SAM, BAM, VCF). This HTS workflow manager allows running parallel analysis or global, where several samples will be analysed together. TOGGLe was used on numerous sequencing projects with high number of samples, or/and high depth sequencing. It was shown to be highly adaptable to various biological questions as well as to a large array of computing architecture and data. In this poster, we are going to show how users can enjoy of TOGGLe in their data analysis.

Auteurs et affiliations

• Orjuela Castellanos Julie, CIRAD-BIOS-UMR AGAP (FRA)
• Ravel Sébastien, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0001-6663-782X
• Dereeper Alexis, INRA (FRA)
• Tando Ndomassi, IRD (FRA)
• Sabot François, IRD (FRA)
• Tranchant-Dubreuil Christine, IRD (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/588855/)

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