{"id":"https://openalex.org/W3177485564","doi":"https://doi.org/10.1371/journal.pcbi.1009078","title":"lra: A long read aligner for sequences and contigs","display_name":"lra: A long read aligner for sequences and contigs","publication_year":2021,"publication_date":"2021-06-21","ids":{"openalex":"https://openalex.org/W3177485564","doi":"https://doi.org/10.1371/journal.pcbi.1009078","mag":"3177485564","pmid":"https://pubmed.ncbi.nlm.nih.gov/34153026"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009078","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009078","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1009078","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103062905","display_name":"Jingwen Ren","orcid":"https://orcid.org/0000-0002-3356-3008"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jingwen Ren","raw_affiliation_strings":["Department of Quantitative and Computational Biology (QCB), University of Southern California, Los Angeles, California, the United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3356-3008","affiliations":[{"raw_affiliation_string":"Department of Quantitative and Computational Biology (QCB), University of Southern California, Los Angeles, California, the United States of America","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026460408","display_name":"Mark Chaisson","orcid":"https://orcid.org/0000-0001-5395-1457"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark J. P. Chaisson","raw_affiliation_strings":["Department of Quantitative and Computational Biology (QCB), University of Southern California, Los Angeles, California, the United States of America"],"raw_orcid":"https://orcid.org/0000-0001-5395-1457","affiliations":[{"raw_affiliation_string":"Department of Quantitative and Computational Biology (QCB), University of Southern California, Los Angeles, California, the United States of America","institution_ids":["https://openalex.org/I1174212"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5026460408"],"corresponding_institution_ids":["https://openalex.org/I1174212"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":10.6648,"has_fulltext":false,"cited_by_count":126,"citation_normalized_percentile":{"value":0.99106367,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"17","issue":"6","first_page":"e1009078","last_page":"e1009078"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9926999807357788,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9916999936103821,"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":0.916569709777832},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.7789143323898315},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6763556599617004},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5363712310791016},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.5323246717453003},{"id":"https://openalex.org/keywords/variation","display_name":"Variation (astronomy)","score":0.4843686521053314},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.47717252373695374},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.4349000155925751},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4229072630405426},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4174472689628601},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4146421253681183},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3973059356212616},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.258007287979126},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24466654658317566},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1903764307498932},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06800341606140137},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.06734812259674072}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.916569709777832},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.7789143323898315},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6763556599617004},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5363712310791016},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5323246717453003},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.4843686521053314},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.47717252373695374},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.4349000155925751},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4229072630405426},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4174472689628601},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4146421253681183},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3973059356212616},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.258007287979126},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24466654658317566},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1903764307498932},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06800341606140137},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.06734812259674072},{"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/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"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":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","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":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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","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":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","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":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1009078","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009078","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:34153026","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34153026","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1009078","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009078","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:374191bdee9242da9ac6ee49931ee816","is_oa":true,"landing_page_url":"https://doaj.org/article/374191bdee9242da9ac6ee49931ee816","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 17, Iss 6, p e1009078 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8248648","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8248648","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009078","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009078","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6728877867","display_name":null,"funder_award_id":"U24HG007497.","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G7350967313","display_name":null,"funder_award_id":"1U01HG010973","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G8932470544","display_name":null,"funder_award_id":"U24HG007497","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1493629236","https://openalex.org/W1912672559","https://openalex.org/W1987042978","https://openalex.org/W1990061958","https://openalex.org/W2014660704","https://openalex.org/W2038918619","https://openalex.org/W2087817903","https://openalex.org/W2122598328","https://openalex.org/W2124115696","https://openalex.org/W2137759177","https://openalex.org/W2144560237","https://openalex.org/W2155237411","https://openalex.org/W2166694026","https://openalex.org/W2585955926","https://openalex.org/W2784788330","https://openalex.org/W2788228074","https://openalex.org/W2789843538","https://openalex.org/W2892689606","https://openalex.org/W2908721251","https://openalex.org/W2949062400","https://openalex.org/W2950121474","https://openalex.org/W2952609831","https://openalex.org/W2953174564","https://openalex.org/W2968499116","https://openalex.org/W3022783334","https://openalex.org/W3034581902","https://openalex.org/W3037780309","https://openalex.org/W3042377559","https://openalex.org/W3046401484","https://openalex.org/W3047598142","https://openalex.org/W3101212878","https://openalex.org/W3102863871","https://openalex.org/W3128198169","https://openalex.org/W3130788486","https://openalex.org/W4240302460"],"related_works":["https://openalex.org/W2089480001","https://openalex.org/W2885619582","https://openalex.org/W3167837387","https://openalex.org/W3009176350","https://openalex.org/W2952788979","https://openalex.org/W2949198880","https://openalex.org/W2763726643","https://openalex.org/W1519765314","https://openalex.org/W3005683565","https://openalex.org/W4387503895"],"abstract_inverted_index":{"It":[0],"is":[1,25,55,64,71,156,168],"computationally":[2],"challenging":[3],"to":[4,20,95,142,147,165],"detect":[5],"variation":[6,63,131,149],"by":[7],"aligning":[8],"single-molecule":[9],"sequencing":[10],"(SMS)":[11],"reads,":[12,134],"or":[13],"contigs":[14],"from":[15,99,132,150],"SMS":[16,23],"assemblies.":[17],"One":[18],"approach":[19,115],"efficiently":[21],"align":[22,96],"reads":[24],"sparse":[26],"dynamic":[27],"programming":[28],"(SDP),":[29],"where":[30],"optimal":[31],"chains":[32],"of":[33,47,59,75],"exact":[34],"matches":[35],"are":[36,139],"found":[37],"between":[38],"the":[39,42],"sequence":[40],"and":[41,92,101,118,128,173],"genome.":[43],"While":[44],"straightforward":[45],"implementations":[46],"SDP":[48,86],"penalize":[49],"gaps":[50],"with":[51,87],"a":[52,56,72,81,88,157],"cost":[53,70],"that":[54,84,138],"linear":[57],"function":[58,74],"gap":[60,69,76,90],"length,":[61],"biological":[62],"more":[65],"accurately":[66],"represented":[67],"when":[68,129],"concave":[73],"length.":[77],"We":[78],"have":[79],"developed":[80],"method,":[82],"lra,":[83],"uses":[85],"concave-cost":[89],"penalty,":[91],"used":[93],"lra":[94,167],"long-read":[97],"sequences":[98],"PacBio":[100],"Oxford":[102],"Nanopore":[103],"(ONT)":[104],"instruments":[105],"as":[106,108],"well":[107],"de":[109,151],"novo":[110,152],"assembly":[111,153],"contigs.":[112],"This":[113],"alignment":[114],"increases":[116],"sensitivity":[117],"specificity":[119],"for":[120,124],"SV":[121],"discovery,":[122],"particularly":[123],"variants":[125],"above":[126],"1kb":[127],"discovering":[130],"ONT":[133],"while":[135],"having":[136],"runtime":[137],"comparable":[140],"(1.05-3.76\u00d7)":[141],"current":[143],"methods.":[144],"When":[145],"applied":[146],"calling":[148],"contigs,":[154],"there":[155],"3.2%":[158],"increase":[159],"in":[160,170],"Truvari":[161],"F1":[162],"score":[163],"compared":[164],"minimap2+htsbox.":[166],"available":[169],"bioconda":[171],"(https://anaconda.org/bioconda/lra)":[172],"github":[174],"(https://github.com/ChaissonLab/LRA).":[175]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":27},{"year":2023,"cited_by_count":39},{"year":2022,"cited_by_count":27},{"year":2021,"cited_by_count":11}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}