{"id":"https://openalex.org/W2336321619","doi":"https://doi.org/10.1093/bioinformatics/btw053","title":"Sprites: detection of deletions from sequencing data by re-aligning split reads","display_name":"Sprites: detection of deletions from sequencing data by re-aligning split reads","publication_year":2016,"publication_date":"2016-02-01","ids":{"openalex":"https://openalex.org/W2336321619","doi":"https://doi.org/10.1093/bioinformatics/btw053","mag":"2336321619","pmid":"https://pubmed.ncbi.nlm.nih.gov/26833342"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw053","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw053","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101914916","display_name":"Zhen Zhang","orcid":"https://orcid.org/0000-0003-0623-5866"},"institutions":[{"id":"https://openalex.org/I100286613","display_name":"Hunan Institute of Science and Technology","ror":"https://ror.org/044ysd349","country_code":"CN","type":"education","lineage":["https://openalex.org/I100286613"]},{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen Zhang","raw_affiliation_strings":["1 School of Information Science and Engineering, Central South University, Changsha, 410083, China,","2 College of Information and Communication Engineering, Hunan Institute of Science and Technology, Yueyang, 414006, China,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Information Science and Engineering, Central South University, Changsha, 410083, China,","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"2 College of Information and Communication Engineering, Hunan Institute of Science and Technology, Yueyang, 414006, China,","institution_ids":["https://openalex.org/I100286613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100438360","display_name":"Jianxin Wang","orcid":"https://orcid.org/0000-0003-1516-0480"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Jianxin Wang","raw_affiliation_strings":["1 School of Information Science and Engineering, Central South University, Changsha, 410083, China,","3 Department of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, TX 77030, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Information Science and Engineering, Central South University, Changsha, 410083, China,","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"3 Department of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, TX 77030, USA,","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100422484","display_name":"Junwei Luo","orcid":"https://orcid.org/0000-0001-6841-9893"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junwei Luo","raw_affiliation_strings":["1 School of Information Science and Engineering, Central South University, Changsha, 410083, China,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Information Science and Engineering, Central South University, Changsha, 410083, China,","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059792650","display_name":"Xiaojun Ding","orcid":"https://orcid.org/0000-0001-9837-5975"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaojun Ding","raw_affiliation_strings":["1 School of Information Science and Engineering, Central South University, Changsha, 410083, China,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Information Science and Engineering, Central South University, Changsha, 410083, China,","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033371544","display_name":"Jiancheng Zhong","orcid":"https://orcid.org/0000-0001-6334-9304"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiancheng Zhong","raw_affiliation_strings":["1 School of Information Science and Engineering, Central South University, Changsha, 410083, China,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Information Science and Engineering, Central South University, Changsha, 410083, China,","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111964102","display_name":"Jun Wang","orcid":"https://orcid.org/0009-0008-8475-2934"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Jun Wang","raw_affiliation_strings":["1 School of Information Science and Engineering, Central South University, Changsha, 410083, China,","3 Department of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, TX 77030, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Information Science and Engineering, Central South University, Changsha, 410083, China,","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"3 Department of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, TX 77030, USA,","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091157395","display_name":"Fang\u2010Xiang Wu","orcid":"https://orcid.org/0000-0002-4593-9332"},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Fang-Xiang Wu","raw_affiliation_strings":["4 Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4 Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada and","institution_ids":["https://openalex.org/I32625721"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101465265","display_name":"Yi Pan","orcid":"https://orcid.org/0000-0002-2766-3096"},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yi Pan","raw_affiliation_strings":["5 Department of Computer Science, Georgia State University, Atlanta, GA 30302-4110, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"5 Department of Computer Science, Georgia State University, Atlanta, GA 30302-4110, USA","institution_ids":["https://openalex.org/I181565077"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100438360"],"corresponding_institution_ids":["https://openalex.org/I139660479","https://openalex.org/I181547552"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.2212,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.87659928,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"32","issue":"12","first_page":"1788","last_page":"1796"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9075999855995178,"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":0.9075999855995178,"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":0.04600000008940697,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.010700000450015068,"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/computer-science","display_name":"Computer science","score":0.5603386163711548},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5376478433609009},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5141580104827881},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47899672389030457},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41568806767463684},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3803524971008301},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15382131934165955}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5603386163711548},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5376478433609009},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5141580104827881},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47899672389030457},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41568806767463684},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3803524971008301},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15382131934165955}],"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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw053","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw053","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:26833342","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26833342","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:open-archive.highwire.org:bioinfo:32/12/1788","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/12/1788","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":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1487118672","https://openalex.org/W1595360086","https://openalex.org/W1973067702","https://openalex.org/W2007809666","https://openalex.org/W2052860512","https://openalex.org/W2065817684","https://openalex.org/W2083870688","https://openalex.org/W2085755265","https://openalex.org/W2090144921","https://openalex.org/W2095680943","https://openalex.org/W2096136407","https://openalex.org/W2096791516","https://openalex.org/W2102619694","https://openalex.org/W2103441770","https://openalex.org/W2105510846","https://openalex.org/W2107688500","https://openalex.org/W2108234281","https://openalex.org/W2111350087","https://openalex.org/W2116126626","https://openalex.org/W2123690878","https://openalex.org/W2131813051","https://openalex.org/W2132298698","https://openalex.org/W2133112449","https://openalex.org/W2137779717","https://openalex.org/W2139993758","https://openalex.org/W2143307936","https://openalex.org/W2146005104","https://openalex.org/W2150506261","https://openalex.org/W2154397429","https://openalex.org/W2159640103","https://openalex.org/W2165963439","https://openalex.org/W2169145121","https://openalex.org/W2169508919","https://openalex.org/W2170551349","https://openalex.org/W2171791108","https://openalex.org/W2180318265","https://openalex.org/W4394666350","https://openalex.org/W6674561012"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933","https://openalex.org/W2107233609"],"abstract_inverted_index":{"MOTIVATION:":[0],"Advances":[1],"of":[2,9,16,24,38,137,155,173,203],"next":[3],"generation":[4],"sequencing":[5,71,89,118],"technologies":[6],"and":[7,45,82,95,177,184,213],"availability":[8],"short":[10],"read":[11,125,157],"data":[12,72,186,222],"enable":[13],"the":[14,57,65,132,138,150,156,163,171],"detection":[15],"structural":[17],"variations":[18],"(SVs).":[19],"Deletions,":[20],"an":[21],"important":[22],"type":[23],"SVs,":[25],"have":[26],"been":[27],"suggested":[28],"in":[29,56,146,162,201],"association":[30],"with":[31,43,47,93,97,175,179,197],"genetic":[32],"diseases.":[33],"There":[34],"are":[35,53,223],"three":[36],"types":[37,52],"deletions:":[39],"blunt":[40],"deletions,":[41],"deletions":[42,46,69,87,92,96,116,174,178,195],"microhomologies":[44,176],"microsinsertions.":[48],"The":[49],"last":[50],"two":[51],"very":[54],"common":[55],"human":[58],"genome,":[59],"but":[60],"they":[61],"pose":[62],"difficulty":[63],"for":[64],"detection.":[66],"Furthermore,":[67],"finding":[68],"from":[70,88,117],"remains":[73],"challenging.":[74],"It":[75,120],"is":[76,141,209],"highly":[77],"appealing":[78],"to":[79,85,131,148,169],"develop":[80],"sensitive":[81],"accurate":[83],"methods":[84,200],"detect":[86],"data,":[90],"especially":[91],"microhomology":[94],"microinsertion.":[98],"RESULTS:":[99],"We":[100],"present":[101],"a":[102,122,135,160],"novel":[103],"method":[104],"called":[105],"Sprites":[106,190,208],"(SPlit":[107],"Read":[108],"re-alIgnment":[109],"To":[110],"dEtect":[111],"Structural":[112],"variants)":[113],"which":[114,140],"finds":[115],"data.":[119],"aligns":[121],"whole":[123],"soft-clipping":[124],"rather":[126],"than":[127],"its":[128],"clipped":[129],"part":[130],"target":[133,164],"sequence,":[134],"segment":[136],"reference":[139],"determined":[142],"by":[143],"spanning":[144],"reads,":[145],"order":[147],"find":[149],"longest":[151],"prefix":[152],"or":[153],"suffix":[154],"that":[158,189],"has":[159],"match":[161],"sequence.":[165],"This":[166],"alignment":[167],"aims":[168],"solve":[170],"problem":[172],"microinsertions.":[180],"Using":[181],"both":[182],"simulated":[183],"real":[185],"we":[187],"show":[188],"performs":[191],"better":[192],"on":[193],"detecting":[194],"compared":[196],"other":[198],"current":[199],"terms":[202],"F-score.":[204],"AVAILABILITY":[205],"AND":[206],"IMPLEMENTATION:":[207],"open":[210],"source":[211],"software":[212],"freely":[214],"available":[215,224],"at":[216,225],"https://github.com/zhangzhen/sprites":[217],"CONTACT:":[218],"jxwang@mail.csu.edu.cnSupplementary":[219],"data:":[220],"Supplementary":[221],"Bioinformatics":[226],"online.":[227]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
