{"id":"https://openalex.org/W2143857331","doi":"https://doi.org/10.1093/bioinformatics/btt169","title":"ELOPER: elongation of paired-end reads as a pre-processing tool for improved <i>de novo</i> genome assembly","display_name":"ELOPER: elongation of paired-end reads as a pre-processing tool for improved <i>de novo</i> genome assembly","publication_year":2013,"publication_date":"2013-04-19","ids":{"openalex":"https://openalex.org/W2143857331","doi":"https://doi.org/10.1093/bioinformatics/btt169","mag":"2143857331","pmid":"https://pubmed.ncbi.nlm.nih.gov/23603334"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt169","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt169","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/11/1455/17100069/btt169.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/29/11/1455/17100069/btt169.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5133181553","display_name":"David H. Silver","orcid":"https://orcid.org/0000-0002-3071-304X"},"institutions":[{"id":"https://openalex.org/I174306211","display_name":"Technion \u2013 Israel Institute of Technology","ror":"https://ror.org/03qryx823","country_code":"IL","type":"education","lineage":["https://openalex.org/I174306211"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"David H. Silver","raw_affiliation_strings":["1 Department of Biology, Technion\u2013Israel Institute of Technology, Haifa 32000, Israel and 2Daynix Computing Ltd, Netanya 42317, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biology, Technion\u2013Israel Institute of Technology, Haifa 32000, Israel and 2Daynix Computing Ltd, Netanya 42317, Israel","institution_ids":["https://openalex.org/I174306211"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045598393","display_name":"Shay Ben\u2010Elazar","orcid":"https://orcid.org/0000-0002-1461-9168"},"institutions":[{"id":"https://openalex.org/I174306211","display_name":"Technion \u2013 Israel Institute of Technology","ror":"https://ror.org/03qryx823","country_code":"IL","type":"education","lineage":["https://openalex.org/I174306211"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Shay Ben-Elazar","raw_affiliation_strings":["1 Department of Biology, Technion\u2013Israel Institute of Technology, Haifa 32000, Israel and 2Daynix Computing Ltd, Netanya 42317, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biology, Technion\u2013Israel Institute of Technology, Haifa 32000, Israel and 2Daynix Computing Ltd, Netanya 42317, Israel","institution_ids":["https://openalex.org/I174306211"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080004505","display_name":"Alexei Bogoslavsky","orcid":null},"institutions":[{"id":"https://openalex.org/I174306211","display_name":"Technion \u2013 Israel Institute of Technology","ror":"https://ror.org/03qryx823","country_code":"IL","type":"education","lineage":["https://openalex.org/I174306211"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Alexei Bogoslavsky","raw_affiliation_strings":["1 Department of Biology, Technion\u2013Israel Institute of Technology, Haifa 32000, Israel and 2Daynix Computing Ltd, Netanya 42317, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biology, Technion\u2013Israel Institute of Technology, Haifa 32000, Israel and 2Daynix Computing Ltd, Netanya 42317, Israel","institution_ids":["https://openalex.org/I174306211"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020438925","display_name":"Itai Yanai","orcid":"https://orcid.org/0000-0002-8438-2741"},"institutions":[{"id":"https://openalex.org/I174306211","display_name":"Technion \u2013 Israel Institute of Technology","ror":"https://ror.org/03qryx823","country_code":"IL","type":"education","lineage":["https://openalex.org/I174306211"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Itai Yanai","raw_affiliation_strings":["1 Department of Biology, Technion\u2013Israel Institute of Technology, Haifa 32000, Israel and 2Daynix Computing Ltd, Netanya 42317, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biology, Technion\u2013Israel Institute of Technology, Haifa 32000, Israel and 2Daynix Computing Ltd, Netanya 42317, Israel","institution_ids":["https://openalex.org/I174306211"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5020438925"],"corresponding_institution_ids":["https://openalex.org/I174306211"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4488,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.66695664,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"29","issue":"11","first_page":"1455","last_page":"1457"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9003000259399414,"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":0.9003000259399414,"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":0.016300000250339508,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.016200000420212746,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.7494425177574158},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.7370831370353699},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6810213327407837},{"id":"https://openalex.org/keywords/pairing","display_name":"Pairing","score":0.6472048163414001},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5116499066352844},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4837212860584259},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4398709535598755},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.42179811000823975},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3269602656364441},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20364689826965332},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19092589616775513},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.10953384637832642},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10668513178825378},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07894766330718994}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.7494425177574158},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.7370831370353699},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6810213327407837},{"id":"https://openalex.org/C14103023","wikidata":"https://www.wikidata.org/wiki/Q11681459","display_name":"Pairing","level":3,"score":0.6472048163414001},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5116499066352844},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4837212860584259},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4398709535598755},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.42179811000823975},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3269602656364441},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20364689826965332},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19092589616775513},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.10953384637832642},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10668513178825378},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07894766330718994},{"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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C54101563","wikidata":"https://www.wikidata.org/wiki/Q124131","display_name":"Superconductivity","level":2,"score":0.0}],"mesh":[{"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":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btt169","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt169","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/11/1455/17100069/btt169.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:23603334","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23603334","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/btt169","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt169","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/11/1455/17100069/btt169.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":[{"id":"https://metadata.un.org/sdg/4","score":0.4699999988079071,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":5,"referenced_works":["https://openalex.org/W1966711026","https://openalex.org/W1972924519","https://openalex.org/W2111322078","https://openalex.org/W2144662851","https://openalex.org/W2161546116"],"related_works":["https://openalex.org/W4281620341","https://openalex.org/W2925048800","https://openalex.org/W1992950355","https://openalex.org/W4381279187","https://openalex.org/W2574304546","https://openalex.org/W2200318732","https://openalex.org/W4313598112","https://openalex.org/W2008826985","https://openalex.org/W3128872455","https://openalex.org/W2078447778"],"abstract_inverted_index":{"MOTIVATION:":[0],"Paired-end":[1],"sequencing":[2],"resulting":[3],"in":[4,21],"gapped":[5,42],"short":[6],"reads":[7,73],"is":[8],"commonly":[9],"used":[10],"for":[11,51,60],"de":[12],"novo":[13],"genome":[14],"assembly.":[15],"Assembly":[16],"methods":[17],"use":[18],"paired-end":[19],"sequences":[20,53],"a":[22,48,56],"two-step":[23],"process,":[24],"first":[25],"treating":[26],"each":[27],"read-end":[28],"independently,":[29],"only":[30],"later":[31],"invoking":[32],"the":[33,37,86,107],"pairing":[34],"to":[35,100],"join":[36],"contiguous":[38],"assemblies":[39,103],"(contigs)":[40],"into":[41],"scaffolds.":[43],"Here,":[44],"we":[45],"present":[46],"ELOPER,":[47],"pre-processing":[49,94],"tool":[50],"pair-end":[52],"that":[54,79,93],"produces":[55],"better":[57],"read":[58,95],"library":[59],"assembly":[61],"programs.":[62],"RESULTS:":[63],"ELOPER":[64,80,98],"proceeds":[65],"by":[66],"simultaneously":[67],"considering":[68],"both":[69],"ends":[70],"of":[71,88],"paired":[72],"generating":[74],"elongated":[75],"reads.":[76,89],"We":[77,90],"show":[78],"theoretically":[81],"doubles":[82],"read-lengths":[83],"while":[84],"halving":[85],"number":[87],"provide":[91],"evidence":[92],"libraries":[96],"using":[97],"leads":[99],"considerably":[101],"improved":[102],"as":[104],"predicted":[105],"from":[106],"Lander-Waterman":[108],"model.":[109],"AVAILABILITY:":[110],"http://sourceforge.net/projects/eloper":[111],"SUPPLEMENTARY":[112],"INFORMATION:":[113],"Supplementary":[114],"data":[115],"are":[116],"available":[117],"at":[118],"Bioinformatics":[119],"online.":[120]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2016-06-24T00:00:00"}