{"id":"https://openalex.org/W2100684179","doi":"https://doi.org/10.1093/bioinformatics/btv478","title":"svviz: a read viewer for validating structural variants","display_name":"svviz: a read viewer for validating structural variants","publication_year":2015,"publication_date":"2015-08-18","ids":{"openalex":"https://openalex.org/W2100684179","doi":"https://doi.org/10.1093/bioinformatics/btv478","mag":"2100684179","pmid":"https://pubmed.ncbi.nlm.nih.gov/26286809"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv478","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv478","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/24/3994/17345134/btv478.pdf","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/24/3994/17345134/btv478.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014096760","display_name":"Noah Spies","orcid":"https://orcid.org/0000-0002-6759-9842"},"institutions":[{"id":"https://openalex.org/I1321296531","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416","country_code":"US","type":"funder","lineage":["https://openalex.org/I1321296531","https://openalex.org/I1343035065"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Noah Spies","raw_affiliation_strings":["1 Department of Genetics, Stanford University,","2 Department of Pathology, Stanford University,","3 Genome Scale Measurements Group, National Institute of Standards and Technology, Stanford, CA, USA and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Genetics, Stanford University,","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"2 Department of Pathology, Stanford University,","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"3 Genome Scale Measurements Group, National Institute of Standards and Technology, Stanford, CA, USA and","institution_ids":["https://openalex.org/I1321296531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058903767","display_name":"Justin M. Zook","orcid":"https://orcid.org/0000-0003-2309-8402"},"institutions":[{"id":"https://openalex.org/I1321296531","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416","country_code":"US","type":"funder","lineage":["https://openalex.org/I1321296531","https://openalex.org/I1343035065"]},{"id":"https://openalex.org/I4210147263","display_name":"Material Measurement Laboratory","ror":"https://ror.org/04a0y3b96","country_code":"US","type":"government","lineage":["https://openalex.org/I1321296531","https://openalex.org/I1343035065","https://openalex.org/I4210147263"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Justin M. Zook","raw_affiliation_strings":["4 Genome Scale Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4 Genome Scale Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD, USA","institution_ids":["https://openalex.org/I4210147263","https://openalex.org/I1321296531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091471463","display_name":"Marc Salit","orcid":"https://orcid.org/0000-0003-1624-5195"},"institutions":[{"id":"https://openalex.org/I1321296531","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416","country_code":"US","type":"funder","lineage":["https://openalex.org/I1321296531","https://openalex.org/I1343035065"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marc Salit","raw_affiliation_strings":["3 Genome Scale Measurements Group, National Institute of Standards and Technology, Stanford, CA, USA and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Genome Scale Measurements Group, National Institute of Standards and Technology, Stanford, CA, USA and","institution_ids":["https://openalex.org/I1321296531"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069064297","display_name":"Arend Sidow","orcid":"https://orcid.org/0000-0002-8287-331X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arend Sidow","raw_affiliation_strings":["1 Department of Genetics, Stanford University,","2 Department of Pathology, Stanford University,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Genetics, Stanford University,","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"2 Department of Pathology, Stanford University,","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5014096760"],"corresponding_institution_ids":["https://openalex.org/I1321296531","https://openalex.org/I97018004"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.6605,"has_fulltext":true,"cited_by_count":61,"citation_normalized_percentile":{"value":0.93286806,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"31","issue":"24","first_page":"3994","last_page":"3996"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.7947999835014343,"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"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.7947999835014343,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.15520000457763672,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.020099999383091927,"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/visualization","display_name":"Visualization","score":0.6529916524887085},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6517118811607361},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6511404514312744},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.5762614011764526},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5164473056793213},{"id":"https://openalex.org/keywords/zygosity","display_name":"Zygosity","score":0.4544856548309326},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45412248373031616},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.440204381942749},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.422943115234375},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.3583287298679352},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.34324607253074646},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33103740215301514},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3227804899215698},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2717832922935486},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2031075358390808},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11094388365745544}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6529916524887085},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6517118811607361},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6511404514312744},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.5762614011764526},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5164473056793213},{"id":"https://openalex.org/C197845989","wikidata":"https://www.wikidata.org/wiki/Q13048280","display_name":"Zygosity","level":2,"score":0.4544856548309326},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45412248373031616},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.440204381942749},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.422943115234375},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3583287298679352},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34324607253074646},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33103740215301514},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3227804899215698},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2717832922935486},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2031075358390808},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11094388365745544}],"mesh":[{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv478","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv478","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/24/3994/17345134/btv478.pdf","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26286809","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26286809","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:CiteSeerX.psu:10.1.1.966.8013","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.966.8013","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://biorxiv.org/content/biorxiv/early/2015/03/07/016063.full.pdf","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/24/3994","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/24/3994","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv478","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv478","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/24/3994/17345134/btv478.pdf","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332178","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100684179.pdf","grobid_xml":"https://content.openalex.org/works/W2100684179.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W2012016911","https://openalex.org/W2021341670","https://openalex.org/W2066852475","https://openalex.org/W2107318366","https://openalex.org/W2111890322","https://openalex.org/W2130753511","https://openalex.org/W2132341951","https://openalex.org/W2147733682","https://openalex.org/W3098304617"],"related_works":["https://openalex.org/W4361984506","https://openalex.org/W2730300917","https://openalex.org/W2905833392","https://openalex.org/W1759033142","https://openalex.org/W2189508481","https://openalex.org/W3138732900","https://openalex.org/W2158100429","https://openalex.org/W2076774832","https://openalex.org/W3157132971","https://openalex.org/W2972815725"],"abstract_inverted_index":{"UNLABELLED:":[0],"Visualizing":[1],"read":[2,23,110],"alignments":[3],"is":[4,148],"the":[5,51,55,62,74,79,101,117],"most":[6,108,140],"effective":[7],"way":[8],"to":[9,34,107],"validate":[10],"candidate":[11,36],"structural":[12],"variants":[13],"(SVs)":[14],"with":[15,100],"existing":[16],"data.":[17],"We":[18],"present":[19],"svviz,":[20],"a":[21,35,86,92,122],"sequencing":[22,142],"visualizer":[24],"for":[25,44,119],"SVs":[26],"that":[27,68],"sorts":[28],"and":[29,65,131,152],"displays":[30],"only":[31],"reads":[32,67],"relevant":[33,46],"SV.":[37],"svviz":[38,136,147],"works":[39],"by":[40],"searching":[41],"input":[42],"bam(s)":[43],"potentially":[45],"reads,":[47],"realigning":[48],"them":[49],"against":[50,121],"inferred":[52],"sequence":[53],"of":[54,78,96,134],"putative":[56,123],"variant":[57],"allele":[58,64,71],"as":[59,61],"well":[60],"reference":[63,103],"identifying":[66],"match":[69],"one":[70],"better":[72],"than":[73],"other.":[75],"Separate":[76],"views":[77],"two":[80],"alleles":[81],"are":[82],"then":[83],"displayed":[84],"in":[85,150],"scrollable":[87],"web":[88],"browser":[89,113],"view,":[90],"enabling":[91],"more":[93],"intuitive":[94],"visualization":[95],"each":[97],"allele,":[98],"compared":[99],"single":[102],"genome-based":[104],"view":[105,114],"common":[106],"current":[109],"browsers.":[111],"The":[112],"facilitates":[115],"examining":[116],"evidence":[118],"or":[120],"variant,":[124],"estimating":[125],"zygosity,":[126],"visualizing":[127],"affected":[128],"genomic":[129],"annotations":[130],"manual":[132],"refinement":[133],"breakpoints.":[135],"supports":[137],"data":[138],"from":[139,155],"modern":[141],"platforms.":[143],"AVAILABILITY":[144],"AND":[145],"IMPLEMENTATION:":[146],"implemented":[149],"python":[151],"freely":[153],"available":[154],"http://svviz.github.io/.":[156]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
