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

Singer, Jochen and Ruscheweyh, Hans-Joachim and Hofmann, Ariane L. and Thurnherr, Thomas and Singer, Franziska and Toussaint, Nora C. and Ng, Charlotte K. Y. and Piscuoglio, Salvatore and Beisel, Christian and Christofori, Gerhard and Dummer, Reinhard and Hall, Michael N. and Krek, Wilhelm and Levesque, Mitchell and Manz, Markus G. and Moch, Holger and Papassotiropoulos, Andreas and Stekhoven, Daniel J. and Wild, Peter and Wüst, Thomas and Rinn, Bernd and Beerenwinkel, Niko. (2018) NGS-pipe: a flexible, easily extendable, and highly configurable framework for NGS analysis. Bioinformatics , 34 (1). pp. 107-108.

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Official URL: http://edoc.unibas.ch/56308/

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Abstract

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.; 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.
https://github.com/cbg-ethz/NGS-pipe
niko.beerenwinkel@bsse.ethz.ch
Faculties and Departments:03 Faculty of Medicine
03 Faculty of Medicine > Bereich Querschnittsfächer (Klinik) > Pathologie USB
03 Faculty of Medicine > Departement Klinische Forschung > Bereich Querschnittsfächer (Klinik) > Pathologie USB
05 Faculty of Science > Departement Biozentrum > Growth & Development > Biochemistry (Hall)
UniBasel Contributors:Hall, Michael N. and Piscuoglio, Salvatore
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Oxford University Press
ISSN:1367-4803
e-ISSN:1367-4811
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
Identification Number:
Last Modified:28 Jan 2019 16:19
Deposited On:12 Oct 2017 08:48

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