{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T20:19:36Z","timestamp":1773346776283,"version":"3.50.1"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2021,2,5]],"date-time":"2021-02-05T00:00:00Z","timestamp":1612483200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome","doi-asserted-by":"publisher","award":["100956\/Z\/13\/Z"],"award-info":[{"award-number":["100956\/Z\/13\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome","doi-asserted-by":"publisher","award":["201535\/Z\/16\/Z"],"award-info":[{"award-number":["201535\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome","doi-asserted-by":"publisher","award":["206194"],"award-info":[{"award-number":["206194"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ETH Domain","award":["#2017-201"],"award-info":[{"award-number":["#2017-201"]}]},{"name":"European Joint Programme on Rare Diseases","award":["#825575"],"award-info":[{"award-number":["#825575"]}]},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","award":["#1113531"],"award-info":[{"award-number":["#1113531"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Medical Research Future Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The majority of genome analysis tools and pipelines require data to be decrypted for access. This potentially leaves sensitive genetic data exposed, either because the unencrypted data is not removed after analysis, or because the data leaves traces on the permanent storage medium.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>: We defined a file container specification enabling direct byte-level compatible random access to encrypted genetic data stored in community standards such as SAM\/BAM\/CRAM\/VCF\/BCF. By standardizing this format, we show how it can be added as a native file format to genomic libraries, enabling direct analysis of encrypted data without the need to create a decrypted copy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The Crypt4GH specification can be found at: http:\/\/samtools.github.io\/hts-specs\/crypt4gh.pdf.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab087","type":"journal-article","created":{"date-parts":[[2021,2,3]],"date-time":"2021-02-03T23:59:51Z","timestamp":1612396791000},"page":"2753-2754","source":"Crossref","is-referenced-by-count":15,"title":["Crypt4GH: a file format standard enabling native access to encrypted data"],"prefix":"10.1093","volume":"37","author":[{"given":"Alexander","family":"Senf","sequence":"first","affiliation":[{"name":"European Bioinformatics Institute, Wellcome Genome Campus , Hinxton CB10 1SD, UK"},{"name":"Enthought, Inc. , 200 W Cesar Chavez, Suite 202, Austin, TX 78701, USA"}]},{"given":"Robert","family":"Davies","sequence":"additional","affiliation":[{"name":"Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton CB10 1SA, UK"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Haziza","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"}]},{"given":"John","family":"Marshall","sequence":"additional","affiliation":[{"name":"Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow , Glasgow G61 1QH, UK"}]},{"given":"Juan","family":"Troncoso-Pastoriza","sequence":"additional","affiliation":[{"name":"School of Computer and Communication Sciences, EPFL (Ecole polytechnique f\u00e9d\u00e9rale de Lausanne) , EPFL IC IINFCOM LDS, BC 266 (B\u00e2timent BC), Lausanne CH-1015, Switzerland"}]},{"given":"Oliver","family":"Hofmann","sequence":"additional","affiliation":[{"name":"University of Melbourne, Centre for Cancer Research, Victorian Comprehensive Cancer Centre , 305 Grattan Street, Melbourne, VIC 3000, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7532-6898","authenticated-orcid":false,"given":"Thomas M.","family":"Keane","sequence":"additional","affiliation":[{"name":"European Bioinformatics Institute, Wellcome Genome Campus , Hinxton CB10 1SD, UK"},{"name":"School of Life Sciences, University of Nottingham , Nottingham NG7 2RD, UK"}]}],"member":"286","published-online":{"date-parts":[[2021,2,5]]},"reference":[{"key":"2023051609205494500_btab087-B1","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1093\/bioinformatics\/bty492","article-title":"htsget: a protocol for securely streaming genomic data","volume":"35","author":"Kelleher","year":"2019","journal-title":"Bioinformatics"},{"key":"2023051609205494500_btab087-B2","article-title":"Ultra-fast homomorphic encryption models enable secure outsourcing of genotype imputation","author":"Kim","year":"2020","journal-title":"bioRxiv"},{"key":"2023051609205494500_btab087-B3","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1093\/bioinformatics\/bty645","article-title":"CRYFA: a secure encryption tool for genomic 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Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab087\/36291617\/btab087.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/17\/2753\/50339113\/btab087.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/17\/2753\/50339113\/btab087.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T09:23:44Z","timestamp":1684229024000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/17\/2753\/6129091"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,2,5]]},"references-count":5,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2021,9,9]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab087","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,9,1]]},"published":{"date-parts":[[2021,2,5]]}}}