{"id":"https://openalex.org/W3047757922","doi":"https://doi.org/10.1145/3404397.3404445","title":"SWMapper: Scalable Read Mapper on SunWay TaihuLight","display_name":"SWMapper: Scalable Read Mapper on SunWay TaihuLight","publication_year":2020,"publication_date":"2020-08-08","ids":{"openalex":"https://openalex.org/W3047757922","doi":"https://doi.org/10.1145/3404397.3404445","mag":"3047757922"},"language":"en","primary_location":{"id":"doi:10.1145/3404397.3404445","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3404397.3404445","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"49th International Conference on Parallel Processing - ICPP","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5038527513","display_name":"Kai Xu","orcid":"https://orcid.org/0000-0002-0907-2671"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Kai Xu","raw_affiliation_strings":["Shandong University, China"],"affiliations":[{"raw_affiliation_string":"Shandong University, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003075115","display_name":"Xiaohui Duan","orcid":"https://orcid.org/0000-0002-1913-6683"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaohui Duan","raw_affiliation_strings":["Shandong University, China"],"affiliations":[{"raw_affiliation_string":"Shandong University, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101536417","display_name":"Xiangxu Meng","orcid":"https://orcid.org/0000-0001-7290-5659"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangxu Meng","raw_affiliation_strings":["Shandong University, China"],"affiliations":[{"raw_affiliation_string":"Shandong University, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100354048","display_name":"Xin Li","orcid":"https://orcid.org/0009-0009-5315-332X"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Li","raw_affiliation_strings":["Shandong University, China"],"affiliations":[{"raw_affiliation_string":"Shandong University, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bertil Schmidt","raw_affiliation_strings":["Johannes Gutenberg University, Germany"],"affiliations":[{"raw_affiliation_string":"Johannes Gutenberg University, Germany","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100620772","display_name":"Weiguo Liu","orcid":"https://orcid.org/0000-0001-8834-0453"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiguo Liu","raw_affiliation_strings":["Shandong University, China"],"affiliations":[{"raw_affiliation_string":"Shandong University, China","institution_ids":["https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5038527513"],"corresponding_institution_ids":["https://openalex.org/I154099455"],"apc_list":null,"apc_paid":null,"fwci":0.1326,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.53886971,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"31","issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9983999729156494,"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":0.9983999729156494,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.996399998664856,"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":0.796403169631958},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.7503429055213928},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7359438538551331},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5965194702148438},{"id":"https://openalex.org/keywords/xeon","display_name":"Xeon","score":0.5492043495178223},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.514432966709137},{"id":"https://openalex.org/keywords/performance-improvement","display_name":"Performance improvement","score":0.4197552800178528},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14358866214752197}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.796403169631958},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.7503429055213928},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7359438538551331},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5965194702148438},{"id":"https://openalex.org/C145108525","wikidata":"https://www.wikidata.org/wiki/Q656154","display_name":"Xeon","level":2,"score":0.5492043495178223},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.514432966709137},{"id":"https://openalex.org/C2778915421","wikidata":"https://www.wikidata.org/wiki/Q3643177","display_name":"Performance improvement","level":2,"score":0.4197552800178528},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14358866214752197},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3404397.3404445","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3404397.3404445","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"49th International Conference on Parallel Processing - ICPP","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W26356079","https://openalex.org/W1828154403","https://openalex.org/W1904861952","https://openalex.org/W2005271647","https://openalex.org/W2100751585","https://openalex.org/W2124985265","https://openalex.org/W2132729131","https://openalex.org/W2141978878","https://openalex.org/W2170551349","https://openalex.org/W2297835331","https://openalex.org/W2398924165","https://openalex.org/W2433194246","https://openalex.org/W2728256789","https://openalex.org/W2789228469","https://openalex.org/W2794424798","https://openalex.org/W2795614220","https://openalex.org/W2802282671","https://openalex.org/W2885814935","https://openalex.org/W2889116136","https://openalex.org/W2891325938","https://openalex.org/W2899133614","https://openalex.org/W2902659137","https://openalex.org/W2912012512","https://openalex.org/W2914146963","https://openalex.org/W2963613550","https://openalex.org/W3203992401","https://openalex.org/W4252721932"],"related_works":["https://openalex.org/W3138386522","https://openalex.org/W2499279132","https://openalex.org/W2791177606","https://openalex.org/W4297942731","https://openalex.org/W3205838256","https://openalex.org/W2943610686","https://openalex.org/W2607998022","https://openalex.org/W3210911584","https://openalex.org/W229781084","https://openalex.org/W2068975988"],"abstract_inverted_index":{"With":[0],"the":[1,34,57,107,123,127,150,161,195],"rapid":[2],"development":[3],"of":[4,17,33,42,63,106,126,141,156,179,191,202,213],"next-generation":[5],"sequencing":[6,11],"(NGS)":[7],"technologies,":[8],"high":[9,70],"throughput":[10],"platforms":[12],"continuously":[13],"produce":[14],"large":[15],"amounts":[16],"short":[18],"read":[19,54],"DNA":[20],"data":[21,85,95],"at":[22],"low":[23],"cost.":[24],"Read":[25],"mapping":[26],"is":[27,118],"a":[28,50,80,103,142,154,171,209],"performance-critical":[29],"task,":[30],"being":[31],"one":[32,199],"first":[35],"stages":[36],"required":[37],"for":[38,56,111],"many":[39],"different":[40],"types":[41],"NGS":[43],"analysis":[44],"pipelines.":[45],"We":[46],"present":[47],"SWMapper":[48,135,176],"\u2014":[49],"scalable":[51],"and":[52,97,100,167,182],"efficient":[53],"mapper":[55],"Sunway":[58,144],"TaihuLight":[59,145],"supercomputer.":[60],"A":[61],"number":[62],"optimization":[64],"techniques":[65],"are":[66,77],"proposed":[67],"to":[68,120,194],"achieve":[69,187],"performance":[71,131],"on":[72,149,170,198,215],"its":[73],"heterogeneous":[74],"architecture":[75],"which":[76],"centered":[78],"around":[79],"memory-efficient":[81],"succinct":[82],"hash":[83],"index":[84],"structure":[86],"including":[87],"seed":[88],"filtration,":[89],"duplicate":[90],"removal,":[91],"dynamic":[92],"scheduling,":[93],"asynchronous":[94],"transfer,":[96],"overlapping":[98],"I/O":[99],"computation.":[101],"Furthermore,":[102],"vectorized":[104],"version":[105],"banded":[108],"Myers":[109],"algorithm":[110],"pairwise":[112],"alignment":[113],"with":[114],"256-bit":[115],"vector":[116],"registers":[117],"presented":[119],"fully":[121],"exploit":[122],"computational":[124],"power":[125],"SW26010":[128,204],"processor.":[129],"Our":[130,185],"evaluation":[132],"shows":[133],"that":[134],"using":[136],"all":[137],"4":[138],"compute":[139,200,217],"groups":[140],"single":[143],"node":[146],"outperforms":[147],"S-Aligner":[148],"same":[151],"hardware":[152],"by":[153],"factor":[155],"6.2.":[157],"In":[158],"addition,":[159],"compared":[160,193],"state-of-the-art":[162],"CPU-based":[163],"mappers":[164],"RazerS3,":[165],"BitMapper2,":[166],"Hobbes3":[168],"running":[169],"4-core":[172],"Xeon":[173],"W-2123v3":[174],"CPU,":[175],"achieves":[177],"speedups":[178],"26.5,":[180],"7.8,":[181],"2.6,":[183],"respectively.":[184],"optimizations":[186],"an":[188,203],"aggregated":[189],"speedup":[190],"11":[192],"na\u00efve":[196],"implementation":[197],"group":[201],"processor":[205],"as":[206,208],"well":[207],"strong":[210],"scaling":[211],"efficiency":[212],"74%":[214],"128":[216],"groups.":[218]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
