{"id":"https://openalex.org/W2101548835","doi":"https://doi.org/10.1186/1471-2105-13-s14-s8","title":"GapFiller: a de novo assembly approach to fill the gap within paired reads","display_name":"GapFiller: a de novo assembly approach to fill the gap within paired reads","publication_year":2012,"publication_date":"2012-09-01","ids":{"openalex":"https://openalex.org/W2101548835","doi":"https://doi.org/10.1186/1471-2105-13-s14-s8","mag":"2101548835","pmid":"https://pubmed.ncbi.nlm.nih.gov/23095524"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-s14-s8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s14-s8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S14-S8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S14-S8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090189197","display_name":"Francesca Nadalin","orcid":"https://orcid.org/0000-0002-3886-0896"},"institutions":[{"id":"https://openalex.org/I129043915","display_name":"University of Udine","ror":"https://ror.org/05ht0mh31","country_code":"IT","type":"education","lineage":["https://openalex.org/I129043915"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Francesca Nadalin","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of Udine, Udine 33100, Italy. fnadalin@appliedgenomics.org","Department of Mathematics and Computer Science, University of Udine, Udine, 33100, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Udine, Udine 33100, Italy. fnadalin@appliedgenomics.org","institution_ids":["https://openalex.org/I129043915"]},{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Udine, Udine, 33100, Italy","institution_ids":["https://openalex.org/I129043915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006807738","display_name":"Francesco Vezzi","orcid":"https://orcid.org/0000-0002-0243-0018"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Francesco Vezzi","raw_affiliation_strings":["Science for Life Laboratory, KTH Royal Institute of Technology, Solna 17121, Sweden","Science for Life Laboratory, KTH Royal Institute of Technology, Solna, 17121, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Science for Life Laboratory, KTH Royal Institute of Technology, Solna 17121, Sweden","institution_ids":["https://openalex.org/I86987016"]},{"raw_affiliation_string":"Science for Life Laboratory, KTH Royal Institute of Technology, Solna, 17121, Sweden","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I86987016"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042115100","display_name":"Alberto Policriti","orcid":"https://orcid.org/0000-0001-8502-5896"},"institutions":[{"id":"https://openalex.org/I129043915","display_name":"University of Udine","ror":"https://ror.org/05ht0mh31","country_code":"IT","type":"education","lineage":["https://openalex.org/I129043915"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alberto Policriti","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of Udine, Udine, 33100, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Udine, Udine, 33100, Italy","institution_ids":["https://openalex.org/I129043915"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":6.1804,"has_fulltext":true,"cited_by_count":373,"citation_normalized_percentile":{"value":0.97401205,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"13","issue":"S14","first_page":"S8","last_page":"S8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8845000267028809,"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":0.8845000267028809,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.03229999914765358,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.005799999926239252,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6365333795547485},{"id":"https://openalex.org/keywords/hybrid-genome-assembly","display_name":"Hybrid genome assembly","score":0.6138210892677307},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.5587980151176453},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.5516140460968018},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.5279119610786438},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.44052496552467346},{"id":"https://openalex.org/keywords/k-mer","display_name":"k-mer","score":0.4223973751068115},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.3851284682750702},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36465275287628174},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.34817618131637573},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3280711770057678},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2975042462348938},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24168124794960022},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16791623830795288}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6365333795547485},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.6138210892677307},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5587980151176453},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.5516140460968018},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.5279119610786438},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.44052496552467346},{"id":"https://openalex.org/C2279292","wikidata":"https://www.wikidata.org/wiki/Q6322851","display_name":"k-mer","level":4,"score":0.4223973751068115},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3851284682750702},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36465275287628174},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.34817618131637573},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3280711770057678},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2975042462348938},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24168124794960022},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16791623830795288},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D012242","descriptor_name":"Rhodobacter sphaeroides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012242","descriptor_name":"Rhodobacter sphaeroides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012242","descriptor_name":"Rhodobacter sphaeroides","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","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:10.1186/1471-2105-13-s14-s8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s14-s8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S14-S8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23095524","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23095524","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3439727","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3439727","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-s14-s8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s14-s8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S14-S8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2101548835.pdf","grobid_xml":"https://content.openalex.org/works/W2101548835.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1599079562","https://openalex.org/W1972418517","https://openalex.org/W1972924519","https://openalex.org/W2022986961","https://openalex.org/W2033083661","https://openalex.org/W2044540291","https://openalex.org/W2061338306","https://openalex.org/W2078331392","https://openalex.org/W2085332554","https://openalex.org/W2087064593","https://openalex.org/W2092277118","https://openalex.org/W2096128575","https://openalex.org/W2107164256","https://openalex.org/W2118335502","https://openalex.org/W2127651281","https://openalex.org/W2127768708","https://openalex.org/W2133956160","https://openalex.org/W2135361281","https://openalex.org/W2151671981","https://openalex.org/W2151887651","https://openalex.org/W2157107905","https://openalex.org/W2159946869","https://openalex.org/W2160265768","https://openalex.org/W2161546116","https://openalex.org/W2171475724","https://openalex.org/W2519703809"],"related_works":["https://openalex.org/W2127768708","https://openalex.org/W2213265806","https://openalex.org/W2166654698","https://openalex.org/W2008090296","https://openalex.org/W2079322808","https://openalex.org/W2063158050","https://openalex.org/W2115501618","https://openalex.org/W4210830088","https://openalex.org/W2767590279","https://openalex.org/W3090794301"],"abstract_inverted_index":{"BACKGROUND:":[0],"Next":[1,110],"Generation":[2,111],"Sequencing":[3,112],"technologies":[4],"are":[5,203],"able":[6,217,253],"to":[7,19,27,38,63,84,98,147,170,218,238,254,266,271,282,287,329],"provide":[8],"high":[9,220,248,256],"genome":[10],"coverages":[11,257],"at":[12,51,86],"a":[13,94,107,118,128,133,149,231,246,284,301],"relatively":[14],"low":[15],"cost.":[16],"However,":[17],"due":[18],"limited":[20],"reads'":[21,71],"length":[22,72],"(from":[23,262],"30":[24],"bp":[25,264],"up":[26,265],"200":[28],"bp),":[29],"specific":[30],"bioinformatics":[31],"problems":[32],"have":[33],"become":[34],"even":[35],"more":[36,49],"difficult":[37],"solve.":[39],"De":[40],"novo":[41,320],"assembly":[42,321],"with":[43,65,230,276],"short":[44,249],"reads,":[45],"for":[46,53,318],"example,":[47],"is":[48,83,122,127,146,209,252],"complicated":[50],"least":[52],"two":[54,177],"reasons:":[55],"first,":[56],"the":[57,70,74,87,90,172,176,180,207,212,223,277,307],"overall":[58],"amount":[59],"of":[60,76,89,109,151,179,222,258,303,310,335],"\"noisy\"":[61],"data":[62],"cope":[64],"increased":[66],"and,":[67],"second,":[68],"as":[69,136,295],"decreases":[73],"number":[75,302],"unsolvable":[77],"repeats":[78],"grows.":[79],"Our":[80,183],"work's":[81],"aim":[82],"go":[85],"root":[88],"problem":[91],"by":[92],"providing":[93],"pre-processing":[95,314],"tool":[96],"capable":[97],"produce":[99,148,255],"(in-silico)":[100],"longer":[101,154,260],"and":[102,153,163,195,226],"highly":[103],"accurate":[104,259],"sequences":[105,202,261],"from":[106,132,245],"collection":[108,150],"reads.":[113],"RESULTS:":[114],"In":[115,156,211],"this":[116],"paper":[117],"seed-and-extend":[119],"local":[120],"assembler":[121],"presented.":[123],"The":[124,200,269],"kernel":[125],"algorithm":[126],"loop":[129],"that,":[130],"starting":[131,244],"read":[134],"used":[135],"seed,":[137],"keeps":[138],"extending":[139],"it":[140,296],"using":[141,192],"heuristics":[142],"whose":[143],"main":[144],"goal":[145],"error-free":[152],"sequences.":[155,336],"particular,":[157],"GapFiller":[158,215,291],"carefully":[159],"detects":[160],"reliable":[161],"overlaps":[162],"operates":[164],"clustering":[165],"similar":[166],"reads":[167,198,250],"in":[168,300,324],"order":[169],"reconstruct":[171],"missing":[173],"part":[174],"between":[175],"ends":[178],"same":[181],"insert.":[182],"tool's":[184],"output":[185,201],"has":[186,292],"been":[187],"validated":[188],"on":[189,316],"24":[190],"experiments":[191,213],"both":[193],"simulated":[194],"real":[196],"paired":[197],"datasets.":[199],"declared":[204],"correct":[205],"when":[206],"seed-mate":[208],"found.":[210],"performed,":[214],"was":[216],"extend":[219],"percentages":[221],"processed":[224],"seeds":[225],"find":[227],"their":[228],"mates,":[229],"false":[232],"positives":[233],"rate":[234],"that":[235],"turned":[236,280],"out":[237,281],"be":[239,283,298],"nearly":[240],"negligible.":[241],"CONCLUSIONS:":[242],"GapFiller,":[243],"sufficiently":[247],"coverage,":[251],"300":[263],"3500":[267],"bp).":[268],"procedure":[270],"perform":[272],"safe":[273],"extensions,":[274],"together":[275],"mate-found":[278],"check,":[279],"powerful":[285],"criterion":[286],"guarantee":[288],"contigs'":[289],"correctness.":[290],"further":[293],"potential,":[294],"could":[297],"applied":[299],"different":[304],"scenarios,":[305],"including":[306],"post-processing":[308],"validation":[309],"insertions/deletions":[311],"detection":[312],"pipelines,":[313,322],"routines":[315],"datasets":[317],"de":[319],"or":[323,332],"any":[325],"hierarchical":[326],"approach":[327],"designed":[328],"assemble,":[330],"analyse":[331],"validate":[333],"pools":[334]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":27},{"year":2022,"cited_by_count":25},{"year":2021,"cited_by_count":42},{"year":2020,"cited_by_count":39},{"year":2019,"cited_by_count":42},{"year":2018,"cited_by_count":35},{"year":2017,"cited_by_count":36},{"year":2016,"cited_by_count":39},{"year":2015,"cited_by_count":19},{"year":2014,"cited_by_count":15},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}