An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments

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cg.creator.identifierJorge Duitama: 0000-0002-9105-6266
cg.creator.identifierJoe Tohme: 0000-0003-2765-7101
cg.identifier.doihttps://doi.org/10.1093/nar/gkt1381en
cg.isijournalISI Journalen
cg.issn0305-1048en
cg.issue6en
cg.journalNucleic Acids Researchen
cg.subject.ciatPLANT BREEDINGen
cg.subject.ciatRICEen
cg.subject.ciatGENETIC RESOURCESen
cg.volume42en
dc.contributor.authorDuitama, Jorgeen
dc.contributor.authorQuintero, Juan Camiloen
dc.contributor.authorCruz, Daniel Felipeen
dc.contributor.authorQuintero, Constanzaen
dc.contributor.authorHubmann, Georgen
dc.contributor.authorFoulquié Moreno, Maria R.en
dc.contributor.authorVerstrepen, Kevin J.en
dc.contributor.authorTrevelein, Johan Men
dc.contributor.authorTohme, Joseph M.en
dc.date.accessioned2014-08-06T06:55:02Zen
dc.date.available2014-08-06T06:55:02Zen
dc.identifier.urihttps://hdl.handle.net/10568/41897
dc.titleAn integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experimentsen
dcterms.abstractRecent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis still require important investments in highly skilled personnel. Developing accurate, efficient and user-friendly software packages for HTS data analysis will lead to a more rapid discovery of genomic elements relevant to medical, agricultural and industrial applications. We therefore developed Next-Generation Sequencing Eclipse Plug-in (NGSEP), a new software tool for integrated, efficient and user-friendly detection of single nucleotide variants (SNVs), indels and copy number variants (CNVs). NGSEP includes modules for read alignment, sorting, merging, functional annotation of variants, filtering and quality statistics. Analysis of sequencing experiments in yeast, rice and human samples shows that NGSEP has superior accuracy and efficiency, compared with currently available packages for variants detection. We also show that only a comprehensive and accurate identification of repeat regions and CNVs allows researchers to properly separate SNVs from differences between copies of repeat elements. We expect that NGSEP will become a strong support tool to empower the analysis of sequencing data in a wide range of research projects on different species.en
dcterms.accessRightsOpen Access
dcterms.audienceScientistsen
dcterms.available2014-01-11
dcterms.bibliographicCitationDuitama J, Quintero JC, Cruz DF, Quintero C, Hubmann G, Foulquié-Moreno MR, Verstrepen KJ, Thevelein JM, and Tohme J. 2014. An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments. Nucleic Acids Research. 42 (6): e44en
dcterms.extentpp. e44-e44en
dcterms.issued2014-04-01
dcterms.languageen
dcterms.licenseCC-BY-3.0
dcterms.publisherOxford University Pressen
dcterms.subjectriceen
dcterms.subjectarrozen
dcterms.subjectgenotypesen
dcterms.subjectgenotiposen
dcterms.typeJournal Article

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