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NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis

Singer, Jochen ; Ruscheweyh, Hans-Joachim ; Hofmann, Ariane L. ; Thurnherr, Thomas ; Singer, Franziska ; Toussaint, Nora C. ; Ng, Charlotte K Y. ; Piscuoglio, Salvatore ; Beisel, Christian ; Christofori, Gerhard ; Dummer, Reinhard ; Hall, Michael N. ; Krek, Wilhelm ; Levesque, Mitchell P. ; Manz, Markus G. ; Moch, Holger ; Papassotiropoulos, Andreas ; Stekhoven, Daniel J. ; Wild, Peter ; Wüst, Thomas ; Rinn, Bernd ; Beerenwinkel, Niko ; Berger, Bonnie ; Berger, Bonnie

In: Bioinformatics, 2018, vol. 34, no. 1, p. 107-108

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    Titre
    • NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis
    Auteur
    • Singer, Jochen. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
    • Ruscheweyh, Hans-Joachim. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
    • Hofmann, Ariane L.. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
    • Thurnherr, Thomas. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
    • Singer, Franziska. SIB Swiss Institute of Bioinformatics, Basel, Switzerland
    • Toussaint, Nora C.. SIB Swiss Institute of Bioinformatics, Basel, Switzerland
    • Ng, Charlotte K Y.. Department of Biomedicine, University of Basel, Basel, Switzerland
    • Piscuoglio, Salvatore. Institute of Pathology, University Hospital Basel, Basel, Switzerland
    • Beisel, Christian. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
    • Christofori, Gerhard. Department of Biomedicine, University of Basel, Basel, Switzerland
    • Dummer, Reinhard. Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
    • Hall, Michael N.. Biozentrum, University of Basel, Basel, Switzerland
    • Krek, Wilhelm. Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
    • Levesque, Mitchell P.. Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
    • Manz, Markus G.. Division of Hematology, University Hospital Zurich, Zurich, Switzerland
    • Moch, Holger. Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
    • Papassotiropoulos, Andreas. Division of Molecular Neuroscience, Department of Psychology, Basel, Switzerland
    • Stekhoven, Daniel J.. SIB Swiss Institute of Bioinformatics, Basel, Switzerland
    • Wild, Peter. Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
    • Wüst, Thomas. SIB Swiss Institute of Bioinformatics, Basel, Switzerland
    • Rinn, Bernd. SIB Swiss Institute of Bioinformatics, Basel, Switzerland
    • Beerenwinkel, Niko. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
    • Berger, Bonnie. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
    • Berger, Bonnie. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
    Type de document
    • Postprint
    Identifiant OAI-PMH
    • oai:doc.rero.ch:332504
    Summary
    Abstract Motivation Next-generation sequencing is now an established method in genomics, and massive amounts of sequencing data are being generated on a regular basis. Analysis of the sequencing data is typically performed by lab-specific in-house solutions, but the agreement of results from different facilities is often small. General standards for quality control, reproducibility and documentation are missing. Results We developed NGS-pipe, a flexible, transparent and easy-to-use framework for the design of pipelines to analyze whole-exome, whole-genome and transcriptome sequencing data. NGS-pipe facilitates the harmonization of genomic data analysis by supporting quality control, documentation, reproducibility, parallelization and easy adaptation to other NGS experiments. Availability and implementation https://github.com/cbg-ethz/NGS-pipe