{"id":"https://openalex.org/W2039408705","doi":"https://doi.org/10.1109/bibm.2014.6999126","title":"Konnector: Connecting paired-end reads using a bloom filter de Bruijn graph","display_name":"Konnector: Connecting paired-end reads using a bloom filter de Bruijn graph","publication_year":2014,"publication_date":"2014-11-01","ids":{"openalex":"https://openalex.org/W2039408705","doi":"https://doi.org/10.1109/bibm.2014.6999126","mag":"2039408705"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2014.6999126","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2014.6999126","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5077505259","display_name":"Benjamin P. Vandervalk","orcid":"https://orcid.org/0000-0002-3082-3476"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Benjamin P Vandervalk","raw_affiliation_strings":["Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]},{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028264773","display_name":"Shaun D. Jackman","orcid":"https://orcid.org/0000-0002-9275-5966"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Shaun D Jackman","raw_affiliation_strings":["Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]},{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075329098","display_name":"Anthony Raymond","orcid":null},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Anthony Raymond","raw_affiliation_strings":["Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]},{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111786891","display_name":"Hamid Mohamadi","orcid":null},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Hamid Mohamadi","raw_affiliation_strings":["Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]},{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071511946","display_name":"Chen Yang","orcid":"https://orcid.org/0000-0002-5144-7748"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Chen Yang","raw_affiliation_strings":["Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]},{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022002926","display_name":"Dean Attali","orcid":"https://orcid.org/0000-0002-5645-3493"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Dean A Attali","raw_affiliation_strings":["Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]},{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076845048","display_name":"Justin Chu","orcid":"https://orcid.org/0000-0003-0549-4997"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Justin Chu","raw_affiliation_strings":["Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]},{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102829017","display_name":"Ren\u00e9 L. Warren","orcid":"https://orcid.org/0000-0002-9890-2293"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Rene L Warren","raw_affiliation_strings":["Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]},{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017539699","display_name":"\u0130nan\u00e7 Birol","orcid":"https://orcid.org/0000-0003-0950-7839"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Inanc Birol","raw_affiliation_strings":["Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]},{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada","institution_ids":["https://openalex.org/I1289530486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I1289530486"],"apc_list":null,"apc_paid":null,"fwci":5.5065,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.95134902,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"51","last_page":"58"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9994000196456909,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9811999797821045,"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/T11269","display_name":"Algorithms and Data Compression","score":0.972100019454956,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bloom-filter","display_name":"Bloom filter","score":0.8999809622764587},{"id":"https://openalex.org/keywords/de-bruijn-graph","display_name":"De Bruijn graph","score":0.837918221950531},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7170625925064087},{"id":"https://openalex.org/keywords/de-bruijn-sequence","display_name":"De Bruijn sequence","score":0.5968186855316162},{"id":"https://openalex.org/keywords/byte","display_name":"Byte","score":0.565265953540802},{"id":"https://openalex.org/keywords/hash-function","display_name":"Hash function","score":0.5546106100082397},{"id":"https://openalex.org/keywords/hash-table","display_name":"Hash table","score":0.5220984220504761},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5198565125465393},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4991436004638672},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4847519099712372},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3405100107192993},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.32095223665237427},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.18934446573257446},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1883363425731659},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1334930658340454},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1100648045539856}],"concepts":[{"id":"https://openalex.org/C147224247","wikidata":"https://www.wikidata.org/wiki/Q885373","display_name":"Bloom filter","level":2,"score":0.8999809622764587},{"id":"https://openalex.org/C20218877","wikidata":"https://www.wikidata.org/wiki/Q3066095","display_name":"De Bruijn graph","level":3,"score":0.837918221950531},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7170625925064087},{"id":"https://openalex.org/C170320093","wikidata":"https://www.wikidata.org/wiki/Q1953457","display_name":"De Bruijn sequence","level":2,"score":0.5968186855316162},{"id":"https://openalex.org/C43364308","wikidata":"https://www.wikidata.org/wiki/Q8799","display_name":"Byte","level":2,"score":0.565265953540802},{"id":"https://openalex.org/C99138194","wikidata":"https://www.wikidata.org/wiki/Q183427","display_name":"Hash function","level":2,"score":0.5546106100082397},{"id":"https://openalex.org/C67388219","wikidata":"https://www.wikidata.org/wiki/Q207440","display_name":"Hash table","level":3,"score":0.5220984220504761},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5198565125465393},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4991436004638672},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4847519099712372},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3405100107192993},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.32095223665237427},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.18934446573257446},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1883363425731659},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1334930658340454},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1100648045539856},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2014.6999126","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2014.6999126","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4099999964237213}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320335036","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1966822396","https://openalex.org/W1978173716","https://openalex.org/W2010361633","https://openalex.org/W2014286596","https://openalex.org/W2024528333","https://openalex.org/W2033292629","https://openalex.org/W2065817684","https://openalex.org/W2087064593","https://openalex.org/W2095680943","https://openalex.org/W2101548835","https://openalex.org/W2103441770","https://openalex.org/W2103828958","https://openalex.org/W2103962160","https://openalex.org/W2105656684","https://openalex.org/W2112888168","https://openalex.org/W2115501618","https://openalex.org/W2123845384","https://openalex.org/W2124985265","https://openalex.org/W2126540423","https://openalex.org/W2129744420","https://openalex.org/W2129933858","https://openalex.org/W2130530163","https://openalex.org/W2142027180","https://openalex.org/W2142749416","https://openalex.org/W2143857331","https://openalex.org/W2146005104","https://openalex.org/W2154397429","https://openalex.org/W2156658871","https://openalex.org/W2157107905","https://openalex.org/W2157460239","https://openalex.org/W2160969485","https://openalex.org/W2163830511","https://openalex.org/W2165795500","https://openalex.org/W2168133698","https://openalex.org/W2171531867","https://openalex.org/W4394666350","https://openalex.org/W6678558286"],"related_works":["https://openalex.org/W2562683361","https://openalex.org/W3087469195","https://openalex.org/W2354744388","https://openalex.org/W3125399386","https://openalex.org/W2949121831","https://openalex.org/W2756186577","https://openalex.org/W2735897904","https://openalex.org/W3215786367","https://openalex.org/W2105656684","https://openalex.org/W1908987670"],"abstract_inverted_index":{"Paired-end":[0],"sequencing":[1,33,45],"yields":[2],"a":[3,9,14,75,92,103,106,123,133],"read":[4,44,88],"from":[5,27,213],"each":[6],"end":[7],"of":[8,16,83,127,150,156,166],"DNA":[10],"fragment,":[11],"typically":[12],"leaving":[13],"gap":[15,24,60,86],"unsequenced":[17],"nucleotides":[18,82],"in":[19,30,69,80],"the":[20,31,36,81,84,98,118,137,151,157,164,167,191],"middle.":[21],"Closing":[22],"this":[23],"using":[25,42,102,122],"information":[26],"other":[28],"reads":[29,49],"same":[32],"experiment":[34],"offers":[35],"potential":[37],"to":[38,78,116,159],"generate":[39],"longer":[40],"\u201cpseudo-reads\u201d":[41],"short":[43],"platforms.":[46],"Such":[47],"long":[48],"may":[50],"benefit":[51],"downstream":[52,179],"applications":[53,68],"such":[54],"as":[55],"de":[56,93,99,119],"novo":[57],"sequence":[58,85],"assembly,":[59],"filling,":[61],"and":[62,108,171,174,206,208],"variant":[63],"detection.":[64],"With":[65],"these":[66],"possible":[67],"mind,":[70],"we":[71],"have":[72],"developed":[73],"Konnector,":[74],"software":[76],"tool":[77,158,168,199],"fill":[79],"between":[87],"pairs":[89],"by":[90],"navigating":[91],"Bruijn":[94,100,120],"graph.":[95],"Konnector":[96],"represents":[97,132],"graph":[101,121],"Bloom":[104],"filter,":[105],"probabilistic":[107],"memory-efficient":[109],"data":[110,141],"structure.":[111,142],"Our":[112],"implementation":[113],"is":[114,148,182,200,209],"able":[115],"store":[117],"mean":[124],"1.5":[125],"bytes":[126],"memory":[128,144],"per":[129,146],"k-mer,":[130],"which":[131],"marked":[134],"improvement":[135],"over":[136],"typical":[138],"hash":[139],"table":[140],"The":[143,198],"usage":[145],"k-mer":[147,152],"independent":[149],"length,":[153],"enabling":[154],"application":[155],"large":[160],"genomes.":[161],"We":[162],"report":[163],"performance":[165],"on":[169],"simulated":[170],"experimental":[172],"datasets,":[173],"discuss":[175],"its":[176],"utility":[177],"for":[178,186,211],"analysis.":[180],"Availability-Konnector":[181],"open-source":[183],"software,":[184],"free":[185],"academic":[187,196],"use,":[188],"released":[189],"under":[190],"British":[192],"Columbia":[193],"Cancer":[194],"Agency's":[195],"license.":[197],"included":[201],"with":[202],"ABySS":[203],"version":[204],"1.5.2":[205],"later,":[207],"available":[210],"download":[212],"http://www.bcgsc.ca/platform/bioinfo/software/abyss.":[214]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
