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dc.contributor.authorMünz, Men_US
dc.contributor.authorMahamdallie, Sen_US
dc.contributor.authorYost, Sen_US
dc.contributor.authorRimmer, Aen_US
dc.contributor.authorPoyastro-Pearson, Een_US
dc.contributor.authorStrydom, Aen_US
dc.contributor.authorSeal, Sen_US
dc.contributor.authorRuark, Een_US
dc.contributor.authorRahman, Nen_US
dc.coverage.spatialEnglanden_US
dc.date.accessioned2019-03-05T16:27:49Z
dc.date.issued2018en_US
dc.identifierhttps://www.ncbi.nlm.nih.gov/pubmed/29881786en_US
dc.identifier.citationWellcome Open Res, 2018, 3 pp. 36 - ?en_US
dc.identifier.issn2398-502Xen_US
dc.identifier.urihttps://repository.icr.ac.uk/handle/internal/3135
dc.identifier.doi10.12688/wellcomeopenres.14306.1en_US
dc.description.abstractQuality assurance and quality control are essential for robust next generation sequencing (NGS). Here we present CoverView, a fast, flexible, user-friendly quality evaluation tool for NGS data. CoverView processes mapped sequencing reads and user-specified regions to report depth of coverage, base and mapping quality metrics with increasing levels of detail from a chromosome-level summary to per-base profiles. CoverView can flag regions that do not fulfil user-specified quality requirements, allowing suboptimal data to be systematically and automatically presented for review. It also provides an interactive graphical user interface (GUI) that can be opened in a web browser and allows intuitive exploration of results. We have integrated CoverView into our accredited clinical cancer predisposition gene testing laboratory that uses the TruSight Cancer Panel (TSCP). CoverView has been invaluable for optimisation and quality control of our testing pipeline, providing transparent, consistent quality metric information and automatic flagging of regions that fall below quality thresholds. We demonstrate this utility with TSCP data from the Genome in a Bottle reference sample, which CoverView analysed in 13 seconds. CoverView uses data routinely generated by NGS pipelines, reads standard input formats, and rapidly creates easy-to-parse output text (.txt) files that are customised by a simple configuration file. CoverView can therefore be easily integrated into any NGS pipeline. CoverView and detailed documentation for its use are freely available at github.com/RahmanTeamDevelopment/CoverView/releases and www.icr.ac.uk/CoverView.en_US
dc.format.extent36 - ?en_US
dc.languageengen_US
dc.language.isoengen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.subjectNGSen_US
dc.subjectQSMen_US
dc.subjectQuality Sequencing Minimimumen_US
dc.subjectbase qualityen_US
dc.subjectdepth of coverageen_US
dc.subjectgenetic testingen_US
dc.subjectmapping qualityen_US
dc.subjectquality assuranceen_US
dc.subjectquality controlen_US
dc.titleCoverView: a sequence quality evaluation tool for next generation sequencing data.en_US
dc.typeJournal Article
dcterms.dateAccepted2018-03-27en_US
rioxxterms.versionofrecord10.12688/wellcomeopenres.14306.1en_US
rioxxterms.licenseref.startdate2018en_US
rioxxterms.typeJournal Article/Reviewen_US
dc.relation.isPartOfWellcome Open Resen_US
pubs.notesNot knownen_US
pubs.organisational-group/ICR
pubs.organisational-group/ICR/Primary Group
pubs.organisational-group/ICR/Primary Group/ICR Divisions
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Breast Cancer Research
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Breast Cancer Research/Genetic Susceptibility
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Genetics and Epidemiology
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Genetics and Epidemiology/Genetic Susceptibility
pubs.publication-statusPublished onlineen_US
pubs.volume3en_US
pubs.embargo.termsNot knownen_US
icr.researchteamGenetic Susceptibilityen_US
dc.contributor.icrauthorRahman, Saberaen_US


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