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.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.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.doi http://dx.doi.org/10.1093/bib/bbac136
  • dc.identifier.issn 1477-4054
  • dc.identifier.uri http://hdl.handle.net/10230/53230
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/871075
  • 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.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri https://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword European Genome-Phenome Archive
  • 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.type.version info:eu-repo/semantics/publishedVersion

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