{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,28]],"date-time":"2025-11-28T17:14:49Z","timestamp":1764350089669},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The NARWHAL software pipeline has been developed to automate the primary analysis of Illumina sequencing data. This pipeline combines a new and flexible de-multiplexing tool with open-source aligners and automated quality assessment. The entire pipeline can be run using only one simple sample-sheet for diverse sequencing applications. NARWHAL creates a sample-oriented data structure and outperforms existing tools in speed.<\/jats:p>\n               <jats:p>Availability: \u00a0https:\/\/trac.nbic.nl\/narwhal\/<\/jats:p>\n               <jats:p>Contact: w.vanijcken@erasmusmc.nl<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr613","type":"journal-article","created":{"date-parts":[[2011,11,10]],"date-time":"2011-11-10T06:32:04Z","timestamp":1320906724000},"page":"284-285","source":"Crossref","is-referenced-by-count":41,"title":["NARWHAL, a primary analysis pipeline for NGS data"],"prefix":"10.1093","volume":"28","author":[{"given":"R. W. W.","family":"Brouwer","sequence":"first","affiliation":[{"name":"1 Center for Biomics, Department of Cell Biology, Erasmus Medical Center, Rotterdam and 2Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands"},{"name":"1 Center for Biomics, Department of Cell Biology, Erasmus Medical Center, Rotterdam and 2Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands"}]},{"given":"M. C. G. N.","family":"van den Hout","sequence":"additional","affiliation":[{"name":"1 Center for Biomics, Department of Cell Biology, Erasmus Medical Center, Rotterdam and 2Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands"}]},{"given":"F. G.","family":"Grosveld","sequence":"additional","affiliation":[{"name":"1 Center for Biomics, Department of Cell Biology, Erasmus Medical Center, Rotterdam and 2Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands"}]},{"given":"W. F. J.","family":"van IJcken","sequence":"additional","affiliation":[{"name":"1 Center for Biomics, Department of Cell Biology, Erasmus Medical Center, Rotterdam and 2Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2011,11,8]]},"reference":[{"key":"2023012511501512200_B1","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1186\/1471-2164-12-285","article-title":"ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using next generation sequence","volume":"12","author":"Blanca","year":"2011","journal-title":"BMC Genomics"},{"key":"2023012511501512200_B2","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1101\/gr.4086505","article-title":"Galaxy: a platform for interactive large-scale genome analysis","volume":"15","author":"Giardine","year":"2005","journal-title":"Genome Res."},{"key":"2023012511501512200_B3","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.1141319","article-title":"Genome-wide mapping of in vivo protein-DNA interactions","volume":"316","author":"Johnson","year":"2007","journal-title":"Science"},{"key":"2023012511501512200_B4","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023012511501512200_B5","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511501512200_B6","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511501512200_B7","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 Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/2\/284\/48870270\/bioinformatics_28_2_284.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/2\/284\/48870270\/bioinformatics_28_2_284.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:50:46Z","timestamp":1674647446000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/2\/284\/196659"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,11,8]]},"references-count":7,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2012,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr613","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,1,15]]},"published":{"date-parts":[[2011,11,8]]}}}