{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T21:27:40Z","timestamp":1761514060680,"version":"3.37.3"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2017,8,28]],"date-time":"2017-08-28T00:00:00Z","timestamp":1503878400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["609883"],"award-info":[{"award-number":["609883"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["PZ00P3_168165"],"award-info":[{"award-number":["PZ00P3_168165"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/cbg-ethz\/NGS-pipe<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx540","type":"journal-article","created":{"date-parts":[[2017,8,26]],"date-time":"2017-08-26T11:08:23Z","timestamp":1503745703000},"page":"107-108","source":"Crossref","is-referenced-by-count":26,"title":["NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis"],"prefix":"10.1093","volume":"34","author":[{"given":"Jochen","family":"Singer","sequence":"first","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland"}]},{"given":"Hans-Joachim","family":"Ruscheweyh","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland"},{"name":"Scientific IT Services, ETH Zurich, Basel, Switzerland"}]},{"given":"Ariane L","family":"Hofmann","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland"}]},{"given":"Thomas","family":"Thurnherr","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland"}]},{"given":"Franziska","family":"Singer","sequence":"additional","affiliation":[{"name":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland"},{"name":"NEXUS Personalized Health Technologies, Zurich, Switzerland"}]},{"given":"Nora C","family":"Toussaint","sequence":"additional","affiliation":[{"name":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland"},{"name":"NEXUS Personalized Health Technologies, Zurich, Switzerland"}]},{"given":"Charlotte K Y","family":"Ng","sequence":"additional","affiliation":[{"name":"Department of Biomedicine, University of Basel, Basel, Switzerland"},{"name":"Institute of Pathology, University Hospital Basel, Basel, Switzerland"},{"name":"Division of Gastroenterology and Hepatology, University Hospital Basel, Basel, Switzerland"}]},{"given":"Salvatore","family":"Piscuoglio","sequence":"additional","affiliation":[{"name":"Institute of Pathology, University Hospital Basel, Basel, Switzerland"}]},{"given":"Christian","family":"Beisel","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"}]},{"given":"Gerhard","family":"Christofori","sequence":"additional","affiliation":[{"name":"Department of Biomedicine, University of Basel, Basel, Switzerland"}]},{"given":"Reinhard","family":"Dummer","sequence":"additional","affiliation":[{"name":"Department of Dermatology, University Hospital Zurich, Zurich, Switzerland"}]},{"given":"Michael N","family":"Hall","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Basel, Switzerland"}]},{"given":"Wilhelm","family":"Krek","sequence":"additional","affiliation":[{"name":"Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland"}]},{"given":"Mitchell P","family":"Levesque","sequence":"additional","affiliation":[{"name":"Department of Dermatology, University Hospital Zurich, Zurich, Switzerland"}]},{"given":"Markus G","family":"Manz","sequence":"additional","affiliation":[{"name":"Division of Hematology, University Hospital Zurich, Zurich, Switzerland"}]},{"given":"Holger","family":"Moch","sequence":"additional","affiliation":[{"name":"Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland"}]},{"given":"Andreas","family":"Papassotiropoulos","sequence":"additional","affiliation":[{"name":"Division of Molecular Neuroscience, Department of Psychology, Basel, Switzerland"},{"name":"Transfaculty Research Platform Molecular and Cognitive Neurosciences, Basel, Switzerland"},{"name":"Psychiatric University Clinics University of Basel, Basel, Switzerland"},{"name":"Department Biozentrum, Life Sciences Training Facility, University of Basel, Basel, Switzerland"}]},{"given":"Daniel J","family":"Stekhoven","sequence":"additional","affiliation":[{"name":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland"},{"name":"NEXUS Personalized Health Technologies, Zurich, Switzerland"}]},{"given":"Peter","family":"Wild","sequence":"additional","affiliation":[{"name":"Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland"}]},{"given":"Thomas","family":"W\u00fcst","sequence":"additional","affiliation":[{"name":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland"},{"name":"Scientific IT Services, ETH Zurich, Basel, Switzerland"}]},{"given":"Bernd","family":"Rinn","sequence":"additional","affiliation":[{"name":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland"},{"name":"Scientific IT Services, ETH Zurich, Basel, Switzerland"}]},{"given":"Niko","family":"Beerenwinkel","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2017,8,28]]},"reference":[{"key":"2023020208302639700_btx540-B1","doi-asserted-by":"crossref","first-page":"10001.","DOI":"10.1038\/ncomms10001","article-title":"A comprehensive assessment of somatic mutation 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