{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T09:43:41Z","timestamp":1756460621353,"version":"3.41.2"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2022,4,19]],"date-time":"2022-04-19T00:00:00Z","timestamp":1650326400000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"LaCaixa Foundation","award":["LCF\/PR\/CE20\/50740008"],"award-info":[{"award-number":["LCF\/PR\/CE20\/50740008"]}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020","doi-asserted-by":"publisher","award":["871075"],"award-info":[{"award-number":["871075"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Since its launch in 2008, the European Genome\u2013Phenome 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\u00a0694\u00a0442 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\/).<\/jats:p>","DOI":"10.1093\/bib\/bbac136","type":"journal-article","created":{"date-parts":[[2022,4,14]],"date-time":"2022-04-14T11:16:25Z","timestamp":1649934985000},"source":"Crossref","is-referenced-by-count":4,"title":["A quality control portal for sequencing data deposited at the European genome\u2013phenome archive"],"prefix":"10.1093","volume":"23","author":[{"given":"Dietmar","family":"Fern\u00e1ndez-Orth","sequence":"first","affiliation":[{"name":"European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain"}]},{"given":"Manuel","family":"Rueda","sequence":"additional","affiliation":[{"name":"European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain"}]},{"given":"Babita","family":"Singh","sequence":"additional","affiliation":[{"name":"European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain"}]},{"given":"Mauricio","family":"Moldes","sequence":"additional","affiliation":[{"name":"European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain"}]},{"given":"Aina","family":"Jene","sequence":"additional","affiliation":[{"name":"European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain"}]},{"given":"Marta","family":"Ferri","sequence":"additional","affiliation":[{"name":"European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain"}]},{"given":"Claudia","family":"Vasallo","sequence":"additional","affiliation":[{"name":"European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain"}]},{"given":"Lauren A","family":"Fromont","sequence":"additional","affiliation":[{"name":"European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain"}]},{"given":"Arcadi","family":"Navarro","sequence":"additional","affiliation":[{"name":"European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain"}]},{"given":"Jordi","family":"Rambla","sequence":"additional","affiliation":[{"name":"European Genome-phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona, 08003 Spain"}]}],"member":"286","published-online":{"date-parts":[[2022,4,18]]},"reference":[{"volume-title":"Plant Omics: Trends and Applications","year":"2016","author":"Ari","key":"2022051813175645700_ref1"},{"key":"2022051813175645700_ref2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fgene.2014.00157","article-title":"Quality control on the frontier","volume":"5","author":"Paszkiewicz","year":"2014","journal-title":"Front Genet"},{"key":"2022051813175645700_ref3","doi-asserted-by":"crossref","first-page":"e1007556","DOI":"10.1371\/journal.pcbi.1007556","article-title":"Forest QC: quality control on genetic variants from next-generation sequencing data using random forest","volume":"15","author":"Li","year":"2019","journal-title":"PLoS Comput Biol"},{"key":"2022051813175645700_ref4","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/s13059-021-02294-2","article-title":"seqQscorer: automated quality control of next-generation sequencing data using machine learning","volume":"22","author":"Albrecht","year":"2021","journal-title":"Genome Biol"},{"key":"2022051813175645700_ref5","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/ng.3312","article-title":"The European genome-phenome archive of human data consented for biomedical research","volume":"47","author":"Lappalainen","year":"2015","journal-title":"Nat Genet"},{"key":"2022051813175645700_ref6","first-page":"D980","article-title":"The European genome-phenome archive in 2021","author":"Freeberg","year":"2021","journal-title":"Nucleic Acids 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SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2022051813175645700_ref10","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1101\/gr.114819.110","article-title":"Efficient storage of high throughput DNA sequencing data using reference-based compression","volume":"21","author":"Fritz","year":"2011","journal-title":"Genome Res"},{"key":"2022051813175645700_ref11","doi-asserted-by":"crossref","first-page":"e135","DOI":"10.1093\/nar\/gkz775","article-title":"Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context","volume":"47","author":"Ivanov","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2022051813175645700_ref12","doi-asserted-by":"crossref","first-page":"2489","DOI":"10.1093\/bioinformatics\/bty1007","article-title":"Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing","volume":"35","author":"Rausch","year":"2019","journal-title":"Bioinformatics"},{"key":"2022051813175645700_ref13","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"2022051813175645700_ref14","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"2022051813175645700_ref15","doi-asserted-by":"crossref","first-page":"5370","DOI":"10.1093\/bioinformatics\/btz560","article-title":"Variant QC: a visual quality control report for variant evaluation","volume":"35","author":"Yan","year":"2019","journal-title":"Bioinformatics"},{"key":"2022051813175645700_ref16","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1038\/nmeth.3174","article-title":"bam.iobio: a web-based, real-time, sequence alignment file inspector","volume":"11","author":"Miller","year":"2014","journal-title":"Nat Methods"},{"key":"2022051813175645700_ref17","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"Multi QC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"}],"container-title":["Briefings in 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