{"id":"https://openalex.org/W4404410840","doi":"https://doi.org/10.1109/tcbb.2024.3489478","title":"An Efficient Parallel Sketch-Based Algorithmic Workflow for Mapping Long Reads","display_name":"An Efficient Parallel Sketch-Based Algorithmic Workflow for Mapping Long Reads","publication_year":2024,"publication_date":"2024-11-15","ids":{"openalex":"https://openalex.org/W4404410840","doi":"https://doi.org/10.1109/tcbb.2024.3489478","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811229"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3489478","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3489478","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102943780","display_name":"Tazin Rahman","orcid":"https://orcid.org/0009-0001-8469-0234"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tazin Rahman","raw_affiliation_strings":["Washington State University, Pullman, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington State University, Pullman, WA, USA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054749460","display_name":"Oieswarya Bhowmik","orcid":"https://orcid.org/0009-0005-0041-9914"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Oieswarya Bhowmik","raw_affiliation_strings":["Washington State University, Pullman, WA, USA"],"raw_orcid":"https://orcid.org/0009-0005-0041-9914","affiliations":[{"raw_affiliation_string":"Washington State University, Pullman, WA, USA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"last","author":{"id":null,"display_name":"Ananth Kalyanaraman","orcid":"https://orcid.org/0000-0001-6721-233X"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ananth Kalyanaraman","raw_affiliation_strings":["Washington State University, Pullman, WA, USA"],"raw_orcid":"https://orcid.org/0000-0001-6721-233X","affiliations":[{"raw_affiliation_string":"Washington State University, Pullman, WA, USA","institution_ids":["https://openalex.org/I72951846"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5102943780"],"corresponding_institution_ids":["https://openalex.org/I72951846"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1794204,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"1","first_page":"13","last_page":"26"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10627","display_name":"Advanced Image and Video Retrieval Techniques","score":0.9939000010490417,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10824","display_name":"Image Retrieval and Classification Techniques","score":0.9663000106811523,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sketch","display_name":"Sketch","score":0.8007513284683228},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7557347416877747},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7421098947525024},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.40848276019096375},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.28750187158584595},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.23271861672401428}],"concepts":[{"id":"https://openalex.org/C2779231336","wikidata":"https://www.wikidata.org/wiki/Q7534724","display_name":"Sketch","level":2,"score":0.8007513284683228},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7557347416877747},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7421098947525024},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.40848276019096375},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.28750187158584595},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.23271861672401428}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2024.3489478","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3489478","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811229","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811229","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W92770098","https://openalex.org/W344138311","https://openalex.org/W1579534339","https://openalex.org/W1964377951","https://openalex.org/W1988888548","https://openalex.org/W2014704298","https://openalex.org/W2044033049","https://openalex.org/W2062037904","https://openalex.org/W2105656684","https://openalex.org/W2108435020","https://openalex.org/W2124985265","https://openalex.org/W2132069633","https://openalex.org/W2137759177","https://openalex.org/W2144560237","https://openalex.org/W2157539385","https://openalex.org/W2179507357","https://openalex.org/W2194172909","https://openalex.org/W2346680365","https://openalex.org/W2755804176","https://openalex.org/W2765745983","https://openalex.org/W2767590279","https://openalex.org/W2767874009","https://openalex.org/W2789843538","https://openalex.org/W2807773783","https://openalex.org/W2884798430","https://openalex.org/W2892689606","https://openalex.org/W2950150251","https://openalex.org/W2950354111","https://openalex.org/W2951822379","https://openalex.org/W2953147862","https://openalex.org/W2961460076","https://openalex.org/W2987650093","https://openalex.org/W3045408080","https://openalex.org/W3080997834","https://openalex.org/W3098495126","https://openalex.org/W3102863871","https://openalex.org/W3113574521","https://openalex.org/W3118794393","https://openalex.org/W3208925084","https://openalex.org/W3216997764","https://openalex.org/W4220982887","https://openalex.org/W4225624933","https://openalex.org/W4226289813","https://openalex.org/W4242729757","https://openalex.org/W4385585436","https://openalex.org/W4386272000"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2378994405","https://openalex.org/W2385974820","https://openalex.org/W2373478030","https://openalex.org/W2378679551","https://openalex.org/W3149739944","https://openalex.org/W2392363776","https://openalex.org/W2063051341"],"abstract_inverted_index":{"Long":[0],"read":[1,29,170],"technologies":[2,18],"are":[3],"continuing":[4],"to":[5,42,56,104,135,158,162,175,179,189,211,214],"evolve":[6],"at":[7,192],"a":[8,105,111,127,223,237,249],"rapid":[9],"pace,":[10],"with":[11,24,49,226,239],"the":[12,15,63,68,72,79,98,152,167,209,219],"latest":[13],"of":[14,70,100,107,139,187],"high":[16,25],"fidelity":[17],"delivering":[19],"reads":[20,53,103,161,178,231],"over":[21,248],"10":[22],"Kbp":[23],"accuracy.":[26],"Classical":[27],"long":[28,35,52,73,102,140,160,169,177,230],"assemblers":[30],"produce":[31],"assemblies":[32,46],"directly":[33],"from":[34],"reads.":[36,74,141],"Hybrid":[37],"assembly":[38,171],"workflows":[39],"provide":[40],"ways":[41],"combine":[43],"partially":[44],"constructed":[45],"(or":[47,132],"contigs)":[48],"newly":[50],"sequenced":[51],"in":[54,110,218],"order":[55],"generate":[57],"genomic":[58],"scaffolds.":[59],"Under":[60],"either":[61],"setting,":[62,155,172],"main":[64],"computational":[65],"bottleneck":[66],"is":[67,88],"step":[69,81],"mapping":[71,80,101,138,205,238],"While":[75],"many":[76],"tools":[77],"implement":[78],"through":[82],"overlap":[83],"computations,":[84],"designing":[85],"alignment-free":[86,137],"approaches":[87],"necessary":[89],"for":[90,222],"large-scale":[91],"computations.":[92],"In":[93],"this":[94],"paper,":[95],"we":[96,146],"visit":[97],"problem":[99],"database":[106],"subject":[108],"sequences,":[109],"fast":[112],"and":[113,144,165,195,232,242,245],"accurate":[114],"manner.":[115],"We":[116,182],"present":[117],"an":[118,184],"efficient":[119],"parallel":[120],"algorithmic":[121],"workflow,":[122],"called":[123],"JEM-mapper,":[124],"that":[125,201],"uses":[126],"new":[128],"minimizer-based":[129],"Jaccard":[130],"estimator":[131],"JEM)":[133],"sketch":[134],"perform":[136],"For":[142],"implementation":[143],"evaluation,":[145],"consider":[147],"two":[148],"application":[149],"settings:":[150],"(i)":[151],"hybrid":[153,220],"scaffolding":[154],"which":[156,173],"aims":[157,174],"map":[159,176],"partial":[163],"assemblies;":[164],"(ii)":[166],"classical":[168],"one":[180],"another.":[181],"implemented":[183],"MPI+OpenMP":[185],"version":[186],"JEM-mapper":[188,202,235],"enable":[190],"parallelism":[191],"both":[193],"distributed-":[194],"shared-memory":[196],"layers.":[197],"Experimental":[198],"evaluation":[199],"shows":[200],"produces":[203,236],"high-quality":[204],"while":[206],"significantly":[207],"improving":[208],"time":[210],"solution":[212],"compared":[213],"state-of-the-art":[215,250],"tools;":[216],"e.g.,":[217],"setting":[221],"large":[224],"genome":[225],"429":[227],"K":[228],"HiFi":[229],"98K":[233],"contigs,":[234],"99.41%":[240],"precision":[241],"97.91%":[243],"recall,":[244],"6.9x":[246],"speedup":[247],"mapper.":[251]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
