{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T17:49:37Z","timestamp":1769968177340,"version":"3.49.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Next-generation sequencing technologies have facilitated the study of organisms on a genome-wide scale. A recent method called restriction site associated DNA sequencing (RAD-seq) allows to sample sequence information at reduced complexity across a target genome using the Illumina platform. Single-end RAD-seq has proven to provide a large number of informative genetic markers in reference as well as non-reference organisms.<\/jats:p><jats:p>Results: Here, we present a method for de novo assembly of paired-end RAD-seq data in order to produce extended contigs flanking a restriction site. We were able to reconstruct one-tenth of the guppy genome represented by 200\u2013500 bp contigs associated to EcoRI recognition sites. In addition, these contigs were used as reference allowing the detection of thousands of new polymorphic markers that are informative for mapping and population genetic studies in the guppy.<\/jats:p><jats:p>Availability: A perl and C++ implementation of the method demonstrated in this article is available under http:\/\/guppy.weigelworld.org\/weigeldatabases\/radMarkers\/ as package RApiD.<\/jats:p><jats:p>Contact: \u00a0christine.dreyer@tuebingen.mpg.de<\/jats:p><jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr346","type":"journal-article","created":{"date-parts":[[2011,6,29]],"date-time":"2011-06-29T00:15:25Z","timestamp":1309306525000},"page":"2187-2193","source":"Crossref","is-referenced-by-count":86,"title":["Paired-end RAD-seq for<i>de novo<\/i>assembly and marker design without available reference"],"prefix":"10.1093","volume":"27","author":[{"given":"Eva-Maria","family":"Willing","sequence":"first","affiliation":[{"name":"1 Department of Molecular Biology, Max Planck Institute for Developmental Biology and 2Department of Algorithms in Bioinformatics, University of T\u00fcbingen, Sand 14, 72076 T\u00fcbingen, Germany"}]},{"given":"Margarete","family":"Hoffmann","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Biology, Max Planck Institute for Developmental Biology and 2Department of Algorithms in Bioinformatics, University of T\u00fcbingen, Sand 14, 72076 T\u00fcbingen, Germany"}]},{"given":"Juliane D.","family":"Klein","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Biology, Max Planck Institute for Developmental Biology and 2Department of Algorithms in Bioinformatics, University of T\u00fcbingen, Sand 14, 72076 T\u00fcbingen, Germany"}]},{"given":"Detlef","family":"Weigel","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Biology, Max Planck Institute for Developmental Biology and 2Department of Algorithms in Bioinformatics, University of T\u00fcbingen, Sand 14, 72076 T\u00fcbingen, Germany"}]},{"given":"Christine","family":"Dreyer","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Biology, Max Planck Institute for Developmental Biology and 2Department of Algorithms in Bioinformatics, University of T\u00fcbingen, Sand 14, 72076 T\u00fcbingen, Germany"}]}],"member":"286","published-online":{"date-parts":[[2011,6,27]]},"reference":[{"key":"2023012511511820800_B1","doi-asserted-by":"crossref","first-page":"e3376","DOI":"10.1371\/journal.pone.0003376","article-title":"Rapid SNP discovery and genetic mapping using sequenced RAD markers","volume":"3","author":"Baird","year":"2008","journal-title":"PLoS ONE"},{"key":"2023012511511820800_B2","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1101\/gr.100040.109","article-title":"Accurate detection and genotyping of SNPs utilizing population sequencing data","volume":"20","author":"Bansal","year":"2010","journal-title":"Genome Res."},{"key":"2023012511511820800_B3","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1038\/nmeth.1251","article-title":"Identification of genetic variants using bar-coded multiplexed sequencing","volume":"5","author":"Craig","year":"2008","journal-title":"Nat. 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