{"id":"https://openalex.org/W4410031861","doi":"https://doi.org/10.1186/s12859-025-06129-w","title":"Fast noisy long read alignment with multi-level parallelism","display_name":"Fast noisy long read alignment with multi-level parallelism","publication_year":2025,"publication_date":"2025-05-02","ids":{"openalex":"https://openalex.org/W4410031861","doi":"https://doi.org/10.1186/s12859-025-06129-w","pmid":"https://pubmed.ncbi.nlm.nih.gov/40316905"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06129-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06129-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06129-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06129-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086155819","display_name":"Zeyu Xia","orcid":"https://orcid.org/0000-0001-7047-7005"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zeyu Xia","raw_affiliation_strings":["College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101044975","display_name":"Canqun Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210164952","display_name":"Tianjin haihe hospital","ror":"https://ror.org/05m762q77","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210164952"]},{"id":"https://openalex.org/I4210165734","display_name":"National Supercomputing Center of Tianjin","ror":"https://ror.org/05tngxm14","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210165734"]},{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Canqun Yang","raw_affiliation_strings":["College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China","Haihe Lab of ITAI, 300457, Tianjin, China","National Supercomputer Center in Tianjin, 300457, Tianjin, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China","institution_ids":["https://openalex.org/I170215575"]},{"raw_affiliation_string":"Haihe Lab of ITAI, 300457, Tianjin, China","institution_ids":["https://openalex.org/I4210164952"]},{"raw_affiliation_string":"National Supercomputer Center in Tianjin, 300457, Tianjin, China","institution_ids":["https://openalex.org/I4210165734"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084918125","display_name":"Chenchen Peng","orcid":null},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenchen Peng","raw_affiliation_strings":["College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105397234","display_name":"Yifei Guo","orcid":"https://orcid.org/0000-0002-0161-8617"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yifei Guo","raw_affiliation_strings":["College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025897338","display_name":"Yufei Guo","orcid":"https://orcid.org/0000-0001-7002-1710"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yufei Guo","raw_affiliation_strings":["College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084996912","display_name":"Tao Tang","orcid":"https://orcid.org/0000-0002-9071-137X"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tao Tang","raw_affiliation_strings":["College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010752019","display_name":"Yingbo Cui","orcid":"https://orcid.org/0000-0003-4000-4957"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yingbo Cui","raw_affiliation_strings":["College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China. yingbocui@nudt.edu.cn"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, National University of Defense Technology, 410073, Changsha, China. yingbocui@nudt.edu.cn","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5086155819"],"corresponding_institution_ids":["https://openalex.org/I170215575"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.7058,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.92896438,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"26","issue":"1","first_page":"118","last_page":"118"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9843000173568726,"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":0.970300018787384,"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/computer-science","display_name":"Computer science","score":0.8652006983757019},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7331827282905579},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.7098628282546997},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.6958355903625488},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5965286493301392},{"id":"https://openalex.org/keywords/vectorization","display_name":"Vectorization (mathematics)","score":0.43709200620651245},{"id":"https://openalex.org/keywords/simd","display_name":"SIMD","score":0.4142322540283203},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3350594937801361},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.10674414038658142}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8652006983757019},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7331827282905579},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.7098628282546997},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6958355903625488},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5965286493301392},{"id":"https://openalex.org/C41681595","wikidata":"https://www.wikidata.org/wiki/Q7917855","display_name":"Vectorization (mathematics)","level":2,"score":0.43709200620651245},{"id":"https://openalex.org/C150552126","wikidata":"https://www.wikidata.org/wiki/Q339387","display_name":"SIMD","level":2,"score":0.4142322540283203},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3350594937801361},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.10674414038658142},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"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":"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":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06129-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06129-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06129-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40316905","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40316905","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:3bd0199fb8d24246aa1c0094a63059e1","is_oa":true,"landing_page_url":"https://doaj.org/article/3bd0199fb8d24246aa1c0094a63059e1","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-31 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12049014","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12049014","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06129-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06129-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06129-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5854786607","display_name":null,"funder_award_id":"Tianjin","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G590285543","display_name":null,"funder_award_id":"62102427","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5939423041","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6670834367","display_name":null,"funder_award_id":"2024RC3115","funder_id":"https://openalex.org/F4320330206","funder_display_name":"Science and Technology Program of Hunan Province"},{"id":"https://openalex.org/G7608752429","display_name":null,"funder_award_id":"Talent","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8740608253","display_name":null,"funder_award_id":"6210242","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324150","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11"},{"id":"https://openalex.org/F4320330206","display_name":"Science and Technology Program of Hunan Province","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410031861.pdf","grobid_xml":"https://content.openalex.org/works/W4410031861.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W145805655","https://openalex.org/W1864199185","https://openalex.org/W1983265703","https://openalex.org/W1984222112","https://openalex.org/W1988888548","https://openalex.org/W2007239153","https://openalex.org/W2007664568","https://openalex.org/W2015915218","https://openalex.org/W2068448872","https://openalex.org/W2068659823","https://openalex.org/W2070102345","https://openalex.org/W2087064593","https://openalex.org/W2088961263","https://openalex.org/W2096041635","https://openalex.org/W2103441770","https://openalex.org/W2107824361","https://openalex.org/W2119501327","https://openalex.org/W2121729186","https://openalex.org/W2128310039","https://openalex.org/W2132341951","https://openalex.org/W2132967231","https://openalex.org/W2133098231","https://openalex.org/W2141978199","https://openalex.org/W2147733682","https://openalex.org/W2159139478","https://openalex.org/W2165808215","https://openalex.org/W2191136822","https://openalex.org/W2260037449","https://openalex.org/W2519021971","https://openalex.org/W2607669908","https://openalex.org/W2799394118","https://openalex.org/W2951105277","https://openalex.org/W2952681371","https://openalex.org/W2964045878","https://openalex.org/W3086678357","https://openalex.org/W3163033414","https://openalex.org/W3197178642","https://openalex.org/W3201830280","https://openalex.org/W4213252003","https://openalex.org/W4231539689","https://openalex.org/W4236356242","https://openalex.org/W4319334382","https://openalex.org/W4381327218","https://openalex.org/W4388801332","https://openalex.org/W4406238208"],"related_works":["https://openalex.org/W2891987081","https://openalex.org/W2566637483","https://openalex.org/W2127324789","https://openalex.org/W3024308452","https://openalex.org/W2099629705","https://openalex.org/W2011430815","https://openalex.org/W3138386522","https://openalex.org/W4244894488","https://openalex.org/W2499279132","https://openalex.org/W4285390450"],"abstract_inverted_index":{"Performance":[0],"evaluations":[1],"show":[2],"that":[3],"ParaHAT":[4],"got":[5],"a":[6,13],"10.03x":[7],"speedup":[8],"in":[9],"base-level":[10],"alignment,":[11],"with":[12],"parallel":[14],"acceleration":[15],"ratio":[16],"and":[17,23],"weak":[18],"scalability":[19],"metric":[20],"of":[21],"94.61":[22],"98.98%":[24],"on":[25],"128":[26],"nodes,":[27],"respectively.":[28]},"counts_by_year":[{"year":2025,"cited_by_count":5}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
