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A quality control portal for sequencing data deposited at the European genome-phenome archive

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dc.contributor.author Fernández-Orth, Dietmar
dc.contributor.author Rueda, Manuel
dc.contributor.author Singh, Babita, 1986-
dc.contributor.author Moldes, Mauricio
dc.contributor.author Jene, Aina
dc.contributor.author Ferri, Marta
dc.contributor.author Vasallo, Claudia
dc.contributor.author Fromont, Lauren A.
dc.contributor.author Navarro i Cuartiellas, Arcadi, 1969-
dc.contributor.author Rambla de Argila, Jordi
dc.date.accessioned 2022-05-24T10:33:30Z
dc.date.available 2022-05-24T10:33:30Z
dc.date.issued 2022
dc.identifier.citation Fernández-Orth D, Rueda M, Singh B, Moldes M, Jene A, Marta Ferri et al. A quality control portal for sequencing data deposited at the European genome-phenome archive. Brief Bioinform. 2022 May 13;23(3):bbac136. DOI:10.1093/bib/bbac136
dc.identifier.issn 1477-4054
dc.identifier.uri http://hdl.handle.net/10230/53230
dc.description.abstract Since its launch in 2008, the European Genome-Phenome Archive (EGA) has been leading the archiving and distribution of human identifiable genomic data. In this regard, one of the community concerns is the potential usability of the stored data, as of now, data submitters are not mandated to perform any quality control (QC) before uploading their data and associated metadata information. Here, we present a new File QC Portal developed at EGA, along with QC reports performed and created for 1 694 442 files [Fastq, sequence alignment map (SAM)/binary alignment map (BAM)/CRAM and variant call format (VCF)] submitted at EGA. QC reports allow anonymous EGA users to view summary-level information regarding the files within a specific dataset, such as quality of reads, alignment quality, number and type of variants and other features. Researchers benefit from being able to assess the quality of data prior to the data access decision and thereby, increasing the reusability of data (https://ega-archive.org/blog/data-upcycling-powered-by-ega/).
dc.description.sponsorship Funding: the File QC feature project has received funding from Horizon 2020 ELIXIR-CONVERGE project (grant agreement No 871075), the ELIXIR-FHD-IS and La Caixa Foundation (LCF/PR/CE20/50740008)
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.rights © Dietmar Fernández_orth et al. 2022. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited
dc.rights.uri https://creativecommons.org/licenses/by/4.0/
dc.subject.other Genòmica
dc.title A quality control portal for sequencing data deposited at the European genome-phenome archive
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/bib/bbac136
dc.subject.keyword European Genome-Phenome Archive
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/871075
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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