{"id":"https://openalex.org/W4385269543","doi":"https://doi.org/10.1093/bioinformatics/btad460","title":"Chaining for accurate alignment of erroneous long reads to acyclic variation graphs","display_name":"Chaining for accurate alignment of erroneous long reads to acyclic variation graphs","publication_year":2023,"publication_date":"2023-07-26","ids":{"openalex":"https://openalex.org/W4385269543","doi":"https://doi.org/10.1093/bioinformatics/btad460","pmid":"https://pubmed.ncbi.nlm.nih.gov/37494467"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad460","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad460","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad460/50967888/btad460.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad460/50967888/btad460.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100357282","display_name":"Jun Ma","orcid":"https://orcid.org/0000-0002-6127-000X"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Jun Ma","raw_affiliation_strings":["Department of Computer Science, University of Helsinki , 00014 Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Helsinki , 00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064412838","display_name":"Manuel C\u00e1ceres","orcid":"https://orcid.org/0000-0003-0235-6951"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Manuel C\u00e1ceres","raw_affiliation_strings":["Department of Computer Science, University of Helsinki , 00014 Helsinki, Finland"],"raw_orcid":"https://orcid.org/0000-0003-0235-6951","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Helsinki , 00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091190630","display_name":"Leena Salmela","orcid":"https://orcid.org/0000-0002-0756-543X"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Leena Salmela","raw_affiliation_strings":["Department of Computer Science, University of Helsinki , 00014 Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Helsinki , 00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043558409","display_name":"Veli M\u00e4kinen","orcid":"https://orcid.org/0000-0003-4454-1493"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Veli M\u00e4kinen","raw_affiliation_strings":["Department of Computer Science, University of Helsinki , 00014 Helsinki, Finland"],"raw_orcid":"https://orcid.org/0000-0003-4454-1493","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Helsinki , 00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063897224","display_name":"Alexandru I. Tomescu","orcid":"https://orcid.org/0000-0002-5747-8350"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Alexandru I Tomescu","raw_affiliation_strings":["Department of Computer Science, University of Helsinki , 00014 Helsinki, Finland"],"raw_orcid":"https://orcid.org/0000-0002-5747-8350","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Helsinki , 00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5063897224","https://openalex.org/A5064412838"],"corresponding_institution_ids":["https://openalex.org/I133731052"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3171,"currency":"EUR","value_usd":3419},"fwci":1.5708,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.83039019,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"39","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8026000261306763,"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":0.8026000261306763,"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":0.09139999747276306,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.025200000032782555,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/chaining","display_name":"Chaining","score":0.9044128060340881},{"id":"https://openalex.org/keywords/variation","display_name":"Variation (astronomy)","score":0.6980870962142944},{"id":"https://openalex.org/keywords/directed-acyclic-graph","display_name":"Directed acyclic graph","score":0.617286205291748},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6148794293403625},{"id":"https://openalex.org/keywords/backward-chaining","display_name":"Backward chaining","score":0.4536071717739105},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3375566005706787},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32406365871429443},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.09344109892845154},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.053523749113082886}],"concepts":[{"id":"https://openalex.org/C49020025","wikidata":"https://www.wikidata.org/wiki/Q1059099","display_name":"Chaining","level":2,"score":0.9044128060340881},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.6980870962142944},{"id":"https://openalex.org/C74197172","wikidata":"https://www.wikidata.org/wiki/Q1195339","display_name":"Directed acyclic graph","level":2,"score":0.617286205291748},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6148794293403625},{"id":"https://openalex.org/C129916263","wikidata":"https://www.wikidata.org/wiki/Q1141183","display_name":"Backward chaining","level":4,"score":0.4536071717739105},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3375566005706787},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32406365871429443},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.09344109892845154},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.053523749113082886},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"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/C46743427","wikidata":"https://www.wikidata.org/wiki/Q1341685","display_name":"Inference engine","level":3,"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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"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":"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},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad460","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad460","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad460/50967888/btad460.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37494467","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37494467","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10423031","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10423031","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10423031/pdf/btad460.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad460","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad460","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad460/50967888/btad460.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3111746600","display_name":"Foundations of Safe and Complete Algorithms with Applications","funder_award_id":"322595","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G4335441921","display_name":null,"funder_award_id":"328877","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G434337789","display_name":null,"funder_award_id":"HORIZON2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5330925427","display_name":null,"funder_award_id":"352821","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G6120476676","display_name":"Complete and accurate reconstruction of biological sequences","funder_award_id":"308030","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G6224492464","display_name":null,"funder_award_id":"851093","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7457209830","display_name":null,"funder_award_id":"322595, 328877","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4385269543.pdf"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1520134085","https://openalex.org/W1978981589","https://openalex.org/W1984236772","https://openalex.org/W2054895735","https://openalex.org/W2099844038","https://openalex.org/W2142113273","https://openalex.org/W2144560237","https://openalex.org/W2194172909","https://openalex.org/W2519989212","https://openalex.org/W2547528004","https://openalex.org/W2596937542","https://openalex.org/W2787131599","https://openalex.org/W2789843538","https://openalex.org/W2799595459","https://openalex.org/W2808544288","https://openalex.org/W2888300707","https://openalex.org/W2913934544","https://openalex.org/W2929062889","https://openalex.org/W2952366981","https://openalex.org/W2952746707","https://openalex.org/W2953174564","https://openalex.org/W2992988966","https://openalex.org/W3007365321","https://openalex.org/W3014094413","https://openalex.org/W3088400220","https://openalex.org/W3092652421","https://openalex.org/W3159082119","https://openalex.org/W3178369392","https://openalex.org/W3211833515","https://openalex.org/W4200597270","https://openalex.org/W4205330988","https://openalex.org/W4206067192","https://openalex.org/W4210631930","https://openalex.org/W4255836900","https://openalex.org/W4308735750","https://openalex.org/W4310552159","https://openalex.org/W6775279221","https://openalex.org/W6803499797"],"related_works":["https://openalex.org/W2132414486","https://openalex.org/W2044830634","https://openalex.org/W2114383597","https://openalex.org/W2472912427","https://openalex.org/W4238340239","https://openalex.org/W2767696758","https://openalex.org/W2184441786","https://openalex.org/W2886511220","https://openalex.org/W3105211564","https://openalex.org/W2129428592"],"abstract_inverted_index":{"MOTIVATION:":[0],"Aligning":[1],"reads":[2,146,161,187],"to":[3,103,114,147,170,245],"a":[4,8,45,94,111,117,122,135,140],"variation":[5,37,91,149],"graph":[6,29,246],"is":[7,44,64,102,283],"standard":[9],"task":[10],"in":[11,38,89,99,121,262],"pangenomics,":[12],"with":[13,128,162,234],"downstream":[14],"applications":[15],"such":[16,134],"as":[17],"improving":[18],"variant":[19],"calling.":[20],"While":[21],"the":[22,39,65,83,87,90,100,129,194,255,297],"vg":[23],"toolkit":[24,30],"[Garrison":[25],"et":[26,224],"al.":[27,225],"(Variation":[28],"improves":[31],"read":[32,77,88,181,216],"mapping":[33],"by":[34,74],"representing":[35],"genetic":[36],"reference.":[40],"Nat":[41],"Biotechnol":[42],"2018;36:875-9)]":[43],"popular":[46],"aligner":[47,67,142],"of":[48,68,86,119,133,143,210,214,230,254,274],"short":[49],"reads,":[50,176,212],"GraphAligner":[51,72],"[Rautiainen":[52],"and":[53,57,157,167,177,193,201,208,213,228,239,242,290],"Marschall":[54],"(GraphAligner:":[55],"rapid":[56],"versatile":[58],"sequence-to-graph":[59],"alignment.":[60],"Genome":[61,236],"Biol":[62,237],"2020;21:253-28)]":[63],"state-of-the-art":[66],"erroneous":[69,144],"long":[70,145],"reads.":[71],"works":[73],"finding":[75],"candidate":[76],"occurrences":[78],"based":[79],"on":[80,183,260,276],"individually":[81],"extending":[82],"best":[84],"seeds":[85,120],"graph.":[92],"However,":[93],"more":[95,175,179],"principled":[96],"approach":[97],"recognized":[98],"community":[101],"co-linearly":[104,115],"chain":[105,116],"multiple":[106],"seeds.":[107],"RESULTS:":[108],"We":[109,152,218],"present":[110],"new":[112,141],"algorithm":[113,138],"set":[118],"string":[123],"labeled":[124],"acyclic":[125,148],"graph,":[126],"together":[127],"first":[130],"efficient":[131],"implementation":[132],"co-linear":[136,250],"chaining":[137],"into":[139],"graphs,":[150],"GraphChainer.":[151],"run":[153],"experiments":[154],"aligning":[155],"real":[156,184,202],"simulated":[158,200],"PacBio":[159,185],"CLR":[160,186],"average":[163],"error":[164],"rates":[165],"15%":[166],"5%.":[168],"Compared":[169],"GraphAligner,":[171],"GraphChainer":[172,204,282],"aligns":[173,205],"12-17%":[174],"21-28%":[178],"total":[180,215],"length,":[182],"from":[188,296],"human":[189,196],"chromosomes":[190],"1,":[191],"22,":[192],"whole":[195],"pangenome.":[197],"On":[198],"both":[199],"data,":[203],"between":[206],"95%":[207],"99%":[209],"all":[211],"length.":[217],"also":[219],"show":[220],"that":[221],"minigraph":[222],"[Li":[223],"(The":[226],"design":[227],"construction":[229],"reference":[231],"pangenome":[232],"graphs":[233],"minigraph.":[235],"2020;21:265-19.)]":[238],"minichain":[240],"[Chandra":[241],"Jain":[243],"(Sequence":[244],"alignment":[247],"using":[248],"gap-sensitive":[249],"chaining.":[251],"In:":[252],"Proceedings":[253],"27th":[256],"Annual":[257],"International":[258],"Conference":[259],"Research":[261],"Computational":[263],"Molecular":[264],"Biology":[265],"(RECOMB":[266],"2023).":[267],"Springer,":[268],"2023,":[269],"58-73.)]":[270],"obtain":[271],"an":[272],"accuracy":[273],"<60%":[275],"this":[277],"setting.":[278],"AVAILABILITY":[279],"AND":[280],"IMPLEMENTATION:":[281],"freely":[284],"available":[285],"at":[286],"https://github.com/algbio/GraphChainer.":[287],"The":[288],"datasets":[289],"evaluation":[291],"pipeline":[292],"can":[293],"be":[294],"reached":[295],"previous":[298],"address.":[299]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1}],"updated_date":"2026-08-04T08:18:43.703281","created_date":"2025-10-10T00:00:00"}
