{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T17:14:06Z","timestamp":1732036446932},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2017,1,9]],"date-time":"2017-01-09T00:00:00Z","timestamp":1483920000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis. We also describe important technical extensions. The high throughput executor (HTE) helps to increase the reliability and to reduce manual interventions when processing complex datasets. We also provide a dedicated binary manager that assists users in obtaining the modules\u2019 executables and keeping them up to date. As basis for this actively developed toolbox we use the workflow management software KNIME.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>See http:\/\/ibisngs.github.io\/knime4ngs for nodes and user manual (GPLv3 license)<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx003","type":"journal-article","created":{"date-parts":[[2017,1,4]],"date-time":"2017-01-04T12:05:51Z","timestamp":1483531551000},"page":"1565-1567","source":"Crossref","is-referenced-by-count":6,"title":["KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis"],"prefix":"10.1093","volume":"33","author":[{"given":"Maximilian","family":"Hastreiter","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tim","family":"Jeske","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonathan","family":"Hoser","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Kluge","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaarin","family":"Ahomaa","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marie-Sophie","family":"Friedl","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sebastian J","family":"Kopetzky","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jan-Dominik","family":"Quell","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"H.-Werner","family":"Mewes","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"K\u00fcffner","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,1,9]]},"reference":[{"key":"2023020205104975000_btx003-B1","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome 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KNIME","volume":"27","author":"Lindenbaum","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020205104975000_btx003-B8","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome 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