{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:26Z","timestamp":1740185126913,"version":"3.37.3"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,5,17]],"date-time":"2019-05-17T00:00:00Z","timestamp":1558051200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","award":["U24-CA220441"],"award-info":[{"award-number":["U24-CA220441"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The CRAM format addresses rising DNA storage costs for short-read sequencing by aligning reads to a reference genome and encoding the resulting alignment with Huffman, subexponential, Elias gamma, rANS, gzip and other codes. The CRAM codec is complex, and until now, there has been no JavaScript implementation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed a JavaScript library, Cram-JS, that natively reads and decompresses the CRAM format on-the-fly. The library is used in the JBrowse and IGV-JS genome browsers and can readily be used by other JavaScript applications, in the web browser or in Node.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Cram-JS is written to the ES-6 standard and is available from the GitHub repository at https:\/\/github.com\/GMOD\/cram-js.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz384","type":"journal-article","created":{"date-parts":[[2019,5,10]],"date-time":"2019-05-10T03:20:10Z","timestamp":1557458410000},"page":"4451-4452","source":"Crossref","is-referenced-by-count":2,"title":["Cram-JS: reference-based decompression in node and the browser"],"prefix":"10.1093","volume":"35","author":[{"given":"Robert","family":"Buels","sequence":"first","affiliation":[{"name":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9647-3643","authenticated-orcid":false,"given":"Shihab","family":"Dider","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Colin","family":"Diesh","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James","family":"Robinson","sequence":"additional","affiliation":[{"name":"Broad Institute , Cambridge, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian","family":"Holmes","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,5,17]]},"reference":[{"key":"2023062712533240800_btz384-B1","doi-asserted-by":"crossref","first-page":"2818","DOI":"10.1093\/bioinformatics\/btu390","article-title":"The scramble conversion tool","volume":"30","author":"Bonfield","year":"2014","journal-title":"Bioinformatics"},{"key":"2023062712533240800_btz384-B2","first-page":"337","article-title":"Crumble: reference free Lossy compression of sequence quality values","volume-title":"Bioinformatics.","author":"Bonfield","year":"2018"},{"key":"2023062712533240800_btz384-B3","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s13059-016-0924-1","article-title":"JBrowse: a dynamic web platform for genome visualization and analysis","volume":"17","author":"Buels","year":"2016","journal-title":"Genome Biol"},{"key":"2023062712533240800_btz384-B4","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1093\/bioinformatics\/btr020","article-title":"Dalliance: interactive genome viewing on the web","volume":"27","author":"Down","year":"2011","journal-title":"Bioinformatics"},{"key":"2023062712533240800_btz384-B5","doi-asserted-by":"crossref","first-page":"3124","DOI":"10.1093\/bioinformatics\/btw385","article-title":"GeneCodeq: quality score compression and improved genotyping using a Bayesian framework","volume":"32","author":"Greenfield","year":"2016","journal-title":"Bioinformatics"},{"key":"2023062712533240800_btz384-B6","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":"Hsi-Yang Fritz","year":"2011","journal-title":"Genome Res"},{"key":"2023062712533240800_btz384-B7","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/s12859-016-0932-x","article-title":"MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression","volume":"17","author":"Kim","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"2023062712533240800_btz384-B8","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023062712533240800_btz384-B9","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1093\/bioinformatics\/bts695","article-title":"ChromoZoom: a flexible, fluid, web-based genome browser","volume":"29","author":"Pak","year":"2013","journal-title":"Bioinformatics"},{"year":"2018","author":"Park","key":"2023062712533240800_btz384-B10"},{"key":"2023062712533240800_btz384-B11","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. 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