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NGS-pipe specifications

Information


Unique identifier OMICS_20626
Name NGS-pipe
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline Niko Beerenwinkel

Publication for NGS-pipe

NGS-pipe citation

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

2017
Bioinformatics
PMCID: 5870795
PMID: 28968639
DOI: 10.1093/bioinformatics/btx540

[…] enome analysis by providing best practices (https://software.broadinstitute.org/gatk/best-practices/), but these recommendations are currently not fully implemented computationally.Here, we introduce NGS-pipe, an automated and user friendly framework for the design of pipelines for the analysis of large-scale sequencing data, such as cancer genomics data. NGS-pipe allows to easily develop tailored […]


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NGS-pipe institution(s)
Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland; Scientific IT Services, ETH Zurich, Basel, Switzerland; NEXUS Personalized Health Technologies, Zurich, Switzerland; Biozentrum, University of Basel, Basel, Switzerland; Department of Biomedicine, University of Basel, Basel, Switzerland; Department of Dermatology, University Hospital Zurich, Zurich, Switzerland; Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland; Division of Hematology, University Hospital Zurich, Zurich, Switzerland; Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland; Division of Molecular Neuroscience, Department of Psychology, University of Basel, Basel, Switzerland; Transfaculty Research Platform Molecular and Cognitive Neurosciences, University of Basel, Basel, Switzerland; Psychiatric University Clinics, University of Basel, Basel, Switzerland; Department Biozentrum, Life Sciences Training Facility, University of Basel, Basel, Switzerland; Institute of Pathology, University Hospital Basel, Basel, Switzerland; Division of Gastroenterology and Hepatology, University Hospital of Basel, Basel, Switzerland
NGS-pipe funding source(s)
Supported by the European Research Council [ERC Synergy Grant No. 609883]; SystemsX.ch [RTD Grant 2013/150, IPhD Grant SXPHI0_142005 and SyBIT]; the Swiss Cancer League [KLS-2892-02- 2012]; and by the Swiss National Science Foundation [Ambizione grant number PZ00P3_168165].

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