{"id":"https://openalex.org/W2945760350","doi":"https://doi.org/10.1093/bioinformatics/btz384","title":"Cram-JS: reference-based decompression in node and the browser","display_name":"Cram-JS: reference-based decompression in node and the browser","publication_year":2019,"publication_date":"2019-05-10","ids":{"openalex":"https://openalex.org/W2945760350","doi":"https://doi.org/10.1093/bioinformatics/btz384","mag":"2945760350","pmid":"https://pubmed.ncbi.nlm.nih.gov/31099383"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz384","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz384","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6821367","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053277772","display_name":"Robert Buels","orcid":"https://orcid.org/0000-0002-9605-5895"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Robert Buels","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084133222","display_name":"Shihab Dider","orcid":"https://orcid.org/0000-0001-9647-3643"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shihab Dider","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, Berkeley, CA, USA"],"raw_orcid":"https://orcid.org/0000-0001-9647-3643","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027393785","display_name":"Colin Diesh","orcid":"https://orcid.org/0000-0003-2629-7570"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Colin Diesh","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014218807","display_name":"James Robinson","orcid":"https://orcid.org/0000-0002-2187-5944"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Robinson","raw_affiliation_strings":["Broad Institute , Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute , Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054625887","display_name":"Ian Holmes","orcid":"https://orcid.org/0000-0001-7639-5369"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ian Holmes","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5053277772"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2278,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.50744778,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"35","issue":"21","first_page":"4451","last_page":"4452"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7264000177383423,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7264000177383423,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.02979999966919422,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.026799999177455902,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.8914974331855774},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.833840012550354},{"id":"https://openalex.org/keywords/huffman-coding","display_name":"Huffman coding","score":0.7747936248779297},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5105642080307007},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.44812247157096863},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4297761917114258},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.4135921001434326},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32970210909843445},{"id":"https://openalex.org/keywords/data-compression","display_name":"Data compression","score":0.2053316831588745},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10151109099388123}],"concepts":[{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.8914974331855774},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.833840012550354},{"id":"https://openalex.org/C46900642","wikidata":"https://www.wikidata.org/wiki/Q2647","display_name":"Huffman coding","level":3,"score":0.7747936248779297},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5105642080307007},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.44812247157096863},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4297761917114258},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.4135921001434326},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32970210909843445},{"id":"https://openalex.org/C78548338","wikidata":"https://www.wikidata.org/wiki/Q2493","display_name":"Data compression","level":2,"score":0.2053316831588745},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10151109099388123},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz384","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz384","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31099383","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31099383","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:6821367","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6821367","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:6821367","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6821367","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1668871876","display_name":null,"funder_award_id":"U24 CA220441","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G295682930","display_name":null,"funder_award_id":"R01 HG004483","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4883198729","display_name":null,"funder_award_id":"R01GM080203","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W2021341670","https://openalex.org/W2105114815","https://openalex.org/W2108102223","https://openalex.org/W2108234281","https://openalex.org/W2135216100","https://openalex.org/W2159084616","https://openalex.org/W2283787433","https://openalex.org/W2336957559","https://openalex.org/W2466892528","https://openalex.org/W2615979642","https://openalex.org/W2765185461","https://openalex.org/W2950662571","https://openalex.org/W6748181393"],"related_works":["https://openalex.org/W2160553057","https://openalex.org/W2149603369","https://openalex.org/W4312281161","https://openalex.org/W2315002870","https://openalex.org/W2247762253","https://openalex.org/W2207508605","https://openalex.org/W3048391942","https://openalex.org/W2899280408","https://openalex.org/W2771106662","https://openalex.org/W2249604275"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,34,65],"CRAM":[2,35,62],"format":[3,63],"addresses":[4],"rising":[5],"DNA":[6],"storage":[7],"costs":[8],"for":[9],"short-read":[10],"sequencing":[11],"by":[12,81],"aligning":[13],"reads":[14,58],"to":[15,98],"a":[16,52],"reference":[17],"genome":[18,74],"and":[19,31,39,59,72,76,102],"encoding":[20],"the":[21,61,70,86,99,106],"resulting":[22],"alignment":[23],"with":[24],"Huffman,":[25],"subexponential,":[26],"Elias":[27],"gamma,":[28],"rANS,":[29],"gzip":[30],"other":[32,82],"codes.":[33],"codec":[36],"is":[37,67,96,103],"complex,":[38],"until":[40],"now,":[41],"there":[42],"has":[43],"been":[44],"no":[45],"JavaScript":[46,53,83],"implementation.":[47],"RESULTS:":[48],"We":[49],"have":[50],"developed":[51],"library,":[54],"Cram-JS,":[55],"that":[56],"natively":[57],"decompresses":[60],"on-the-fly.":[64],"library":[66],"used":[68,80],"in":[69,85,90],"JBrowse":[71],"IGV-JS":[73],"browsers":[75],"can":[77],"readily":[78],"be":[79],"applications,":[84],"web":[87],"browser":[88],"or":[89],"Node.":[91],"AVAILABILITY":[92],"AND":[93],"IMPLEMENTATION:":[94],"Cram-JS":[95],"written":[97],"ES-6":[100],"standard":[101],"available":[104],"from":[105],"GitHub":[107],"repository":[108],"at":[109],"https://github.com/GMOD/cram-js.":[110]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
