{"id":"https://openalex.org/W2164558813","doi":"https://doi.org/10.1093/bioinformatics/btu431","title":"Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone","display_name":"Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone","publication_year":2014,"publication_date":"2014-07-14","ids":{"openalex":"https://openalex.org/W2164558813","doi":"https://doi.org/10.1093/bioinformatics/btu431","mag":"2164558813","pmid":"https://pubmed.ncbi.nlm.nih.gov/25028727"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu431","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu431","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/24/3484/7249352/btu431.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":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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/24/3484/7249352/btu431.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033795944","display_name":"Kathrin Trappe","orcid":"https://orcid.org/0000-0002-2887-1575"},"institutions":[{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]},{"id":"https://openalex.org/I4210151462","display_name":"New York Genome Center","ror":"https://ror.org/05wf2ga96","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210151462"]},{"id":"https://openalex.org/I24359323","display_name":"Robert Koch Institute","ror":"https://ror.org/01k5qnb77","country_code":"DE","type":"government","lineage":["https://openalex.org/I24359323"]}],"countries":["DE","US"],"is_corresponding":true,"raw_author_name":"Kathrin Trappe","raw_affiliation_strings":["1 Department of Computer Science, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany, 2 Research Group Bioinformatics (NG4), Robert Koch Institute, 13353 Berlin, Germany and 3 New York Genome Center, New York, NY 10013, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany, 2 Research Group Bioinformatics (NG4), Robert Koch Institute, 13353 Berlin, Germany and 3 New York Genome Center, New York, NY 10013, USA","institution_ids":["https://openalex.org/I24359323","https://openalex.org/I75951250","https://openalex.org/I4210151462"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027987031","display_name":"Anne\u2010Katrin Emde","orcid":"https://orcid.org/0000-0003-2553-2225"},"institutions":[{"id":"https://openalex.org/I24359323","display_name":"Robert Koch Institute","ror":"https://ror.org/01k5qnb77","country_code":"DE","type":"government","lineage":["https://openalex.org/I24359323"]},{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]},{"id":"https://openalex.org/I4210151462","display_name":"New York Genome Center","ror":"https://ror.org/05wf2ga96","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210151462"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Anne-Katrin Emde","raw_affiliation_strings":["1 Department of Computer Science, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany, 2 Research Group Bioinformatics (NG4), Robert Koch Institute, 13353 Berlin, Germany and 3 New York Genome Center, New York, NY 10013, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany, 2 Research Group Bioinformatics (NG4), Robert Koch Institute, 13353 Berlin, Germany and 3 New York Genome Center, New York, NY 10013, USA","institution_ids":["https://openalex.org/I24359323","https://openalex.org/I75951250","https://openalex.org/I4210151462"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072560776","display_name":"Hans\u2010Christian Ehrlich","orcid":"https://orcid.org/0000-0001-5866-5433"},"institutions":[{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]},{"id":"https://openalex.org/I24359323","display_name":"Robert Koch Institute","ror":"https://ror.org/01k5qnb77","country_code":"DE","type":"government","lineage":["https://openalex.org/I24359323"]},{"id":"https://openalex.org/I4210151462","display_name":"New York Genome Center","ror":"https://ror.org/05wf2ga96","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210151462"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Hans-Christian Ehrlich","raw_affiliation_strings":["1 Department of Computer Science, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany, 2 Research Group Bioinformatics (NG4), Robert Koch Institute, 13353 Berlin, Germany and 3 New York Genome Center, New York, NY 10013, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany, 2 Research Group Bioinformatics (NG4), Robert Koch Institute, 13353 Berlin, Germany and 3 New York Genome Center, New York, NY 10013, USA","institution_ids":["https://openalex.org/I24359323","https://openalex.org/I75951250","https://openalex.org/I4210151462"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078948324","display_name":"Knut Reinert","orcid":"https://orcid.org/0000-0003-3078-8129"},"institutions":[{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]},{"id":"https://openalex.org/I24359323","display_name":"Robert Koch Institute","ror":"https://ror.org/01k5qnb77","country_code":"DE","type":"government","lineage":["https://openalex.org/I24359323"]},{"id":"https://openalex.org/I4210151462","display_name":"New York Genome Center","ror":"https://ror.org/05wf2ga96","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210151462"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Knut Reinert","raw_affiliation_strings":["1 Department of Computer Science, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany, 2 Research Group Bioinformatics (NG4), Robert Koch Institute, 13353 Berlin, Germany and 3 New York Genome Center, New York, NY 10013, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany, 2 Research Group Bioinformatics (NG4), Robert Koch Institute, 13353 Berlin, Germany and 3 New York Genome Center, New York, NY 10013, USA","institution_ids":["https://openalex.org/I24359323","https://openalex.org/I75951250","https://openalex.org/I4210151462"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5033795944"],"corresponding_institution_ids":["https://openalex.org/I24359323","https://openalex.org/I4210151462","https://openalex.org/I75951250"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.9825,"has_fulltext":false,"cited_by_count":54,"citation_normalized_percentile":{"value":0.91906079,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"30","issue":"24","first_page":"3484","last_page":"3490"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9957000017166138,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9957000017166138,"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/benchmark","display_name":"Benchmark (surveying)","score":0.7735152244567871},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6445186138153076},{"id":"https://openalex.org/keywords/breakpoint","display_name":"Breakpoint","score":0.5002427101135254},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.43852686882019043},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2102038562297821},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1923012137413025},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12987619638442993},{"id":"https://openalex.org/keywords/chromosomal-translocation","display_name":"Chromosomal translocation","score":0.12975004315376282},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.11711636185646057},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.07205542922019958}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7735152244567871},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6445186138153076},{"id":"https://openalex.org/C206936463","wikidata":"https://www.wikidata.org/wiki/Q634179","display_name":"Breakpoint","level":4,"score":0.5002427101135254},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.43852686882019043},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2102038562297821},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1923012137413025},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12987619638442993},{"id":"https://openalex.org/C138626823","wikidata":"https://www.wikidata.org/wiki/Q916504","display_name":"Chromosomal translocation","level":3,"score":0.12975004315376282},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.11711636185646057},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.07205542922019958},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D014178","descriptor_name":"Translocation, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014178","descriptor_name":"Translocation, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014178","descriptor_name":"Translocation, Genetic","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017384","descriptor_name":"Sequence Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017384","descriptor_name":"Sequence Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017384","descriptor_name":"Sequence Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btu431","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu431","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/24/3484/7249352/btu431.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25028727","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25028727","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu431","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu431","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/24/3484/7249352/btu431.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2164558813.pdf","grobid_xml":"https://content.openalex.org/works/W2164558813.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W26356079","https://openalex.org/W1588822927","https://openalex.org/W1998048394","https://openalex.org/W2013221974","https://openalex.org/W2064469303","https://openalex.org/W2065817684","https://openalex.org/W2075996757","https://openalex.org/W2083870688","https://openalex.org/W2099809434","https://openalex.org/W2103441770","https://openalex.org/W2105510846","https://openalex.org/W2107688500","https://openalex.org/W2107830007","https://openalex.org/W2110171180","https://openalex.org/W2118471291","https://openalex.org/W2121144826","https://openalex.org/W2137779717","https://openalex.org/W2144866873","https://openalex.org/W2146005104","https://openalex.org/W2150506261","https://openalex.org/W2154397429","https://openalex.org/W2155822487","https://openalex.org/W2163549019","https://openalex.org/W2165686834","https://openalex.org/W2171071054","https://openalex.org/W4247053599","https://openalex.org/W6601068097"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2036289360","https://openalex.org/W2003824598","https://openalex.org/W2606481030","https://openalex.org/W2987034282","https://openalex.org/W1979375946","https://openalex.org/W2321977289","https://openalex.org/W2378211422","https://openalex.org/W2102889349","https://openalex.org/W2117117412"],"abstract_inverted_index":{"We":[0,47],"present":[1],"Gustaf":[2,50,81],"(Generic":[3],"mUlti-SpliT":[4],"Alignment":[5],"Finder),":[6],"a":[7,33],"sound":[8],"generic":[9,34],"multi-split":[10,35],"SV":[11,41],"detection":[12],"tool":[13],"that":[14,38,49],"detects":[15],"and":[16,22,90,98,103],"classifies":[17],"deletions,":[18],"inversions,":[19],"dispersed":[20,101],"duplications":[21,102],"translocations":[23],"of":[24,72,100],"\u2265":[25],"30":[26,59],"bp.":[27,80],"Our":[28],"approach":[29],"is":[30,91],"based":[31],"on":[32],"alignment":[36],"strategy":[37],"can":[39],"identify":[40,96],"breakpoints":[42],"with":[43],"base":[44],"pair":[45],"resolution.":[46],"show":[48],"correctly":[51,95],"identifies":[52],"SVs,":[53,73],"especially":[54],"in":[55,87],"the":[56,66],"range":[57],"from":[58],"to":[60,94],"100":[61],"bp,":[62],"which":[63,105],"we":[64],"call":[65],"next-generation":[67],"sequencing":[68],"(NGS)":[69],"twilight":[70],"zone":[71],"as":[74,76,113],"well":[75],"larger":[77],"SVs":[78],">500":[79],"performs":[82],"better":[83],"than":[84],"similar":[85],"tools":[86],"our":[88],"benchmark":[89],"furthermore":[92],"able":[93],"size":[97],"location":[99],"translocations,":[104],"otherwise":[106],"might":[107],"be":[108],"wrongly":[109],"classified,":[110],"for":[111],"example,":[112],"large":[114],"deletions.":[115]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":1}],"updated_date":"2026-03-08T08:50:53.379069","created_date":"2025-10-10T00:00:00"}
