{"id":"https://openalex.org/W4391183524","doi":"https://doi.org/10.1109/asicon58565.2023.10396387","title":"High-Performance Genomic Analysis Heterogeneous System Using OpenCL","display_name":"High-Performance Genomic Analysis Heterogeneous System Using OpenCL","publication_year":2023,"publication_date":"2023-10-24","ids":{"openalex":"https://openalex.org/W4391183524","doi":"https://doi.org/10.1109/asicon58565.2023.10396387"},"language":"en","primary_location":{"id":"doi:10.1109/asicon58565.2023.10396387","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/asicon58565.2023.10396387","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE 15th International Conference on ASIC (ASICON)","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/A5081506948","display_name":"Jianing Gao","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianing Gao","raw_affiliation_strings":["Shanghai Jiao Tong University,Department of Microelectronics and Nanoscience,Shanghai,China","Department of Microelectronics and Nanoscience, Shanghai Jiao Tong University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Department of Microelectronics and Nanoscience,Shanghai,China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Department of Microelectronics and Nanoscience, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010053455","display_name":"Lingyi Liu","orcid":"https://orcid.org/0000-0001-5601-221X"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lingyi Liu","raw_affiliation_strings":["Shanghai Jiao Tong University,Department of Microelectronics and Nanoscience,Shanghai,China","Department of Microelectronics and Nanoscience, Shanghai Jiao Tong University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Department of Microelectronics and Nanoscience,Shanghai,China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Department of Microelectronics and Nanoscience, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025208432","display_name":"Qin Wang","orcid":"https://orcid.org/0000-0003-4846-9468"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qin Wang","raw_affiliation_strings":["Shanghai Jiao Tong University,Department of Microelectronics and Nanoscience,Shanghai,China","Department of Microelectronics and Nanoscience, Shanghai Jiao Tong University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Department of Microelectronics and Nanoscience,Shanghai,China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Department of Microelectronics and Nanoscience, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045693138","display_name":"Naifeng Jing","orcid":"https://orcid.org/0000-0001-8417-5796"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Naifeng Jing","raw_affiliation_strings":["Shanghai Jiao Tong University,Department of Microelectronics and Nanoscience,Shanghai,China","Department of Microelectronics and Nanoscience, Shanghai Jiao Tong University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Department of Microelectronics and Nanoscience,Shanghai,China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Department of Microelectronics and Nanoscience, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008057183","display_name":"Jianfei Jiang","orcid":"https://orcid.org/0000-0002-5521-6197"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianfei Jiang","raw_affiliation_strings":["Shanghai Jiao Tong University,Department of Microelectronics and Nanoscience,Shanghai,China","Department of Microelectronics and Nanoscience, Shanghai Jiao Tong University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Department of Microelectronics and Nanoscience,Shanghai,China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Department of Microelectronics and Nanoscience, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5081506948"],"corresponding_institution_ids":["https://openalex.org/I183067930"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.33911669,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9959999918937683,"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":0.9959999918937683,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9890000224113464,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9674999713897705,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7345403432846069},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3946893513202667},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.33129870891571045}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7345403432846069},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3946893513202667},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.33129870891571045}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/asicon58565.2023.10396387","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/asicon58565.2023.10396387","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE 15th International Conference on ASIC (ASICON)","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":0,"referenced_works":[],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"Nowadays,":[0],"genomic":[1],"analysis":[2],"significantly":[3],"affects":[4],"various":[5],"fields,":[6],"including":[7],"vaccine":[8],"development,":[9],"viral":[10],"evolution":[11],"research,":[12],"precision":[13],"medicine,":[14],"and":[15,91,108,118],"crop":[16],"breeding.":[17],"Minimap2":[18,35,60],"[1]":[19],"is":[20],"widely":[21],"used":[22],"for":[23,41,59,145],"long-read":[24],"sequence":[25],"alignment":[26],"in":[27,34,74,161],"third-generation":[28],"sequencing.":[29],"However,":[30],"the":[31,45,71,75,136,146,150],"chaining":[32,147],"step":[33],"exposes":[36],"a":[37,54,83,97,113,130,141,154],"performance":[38,132],"bottleneck,":[39],"accounting":[40],"nearly":[42],"40%":[43],"of":[44],"overall":[46],"execution":[47],"time.":[48],"In":[49],"this":[50],"paper,":[51],"we":[52,111],"present":[53],"practical":[55],"heterogeneous":[56,114],"acceleration":[57],"system":[58,115,152],"using":[61],"OpenCL.":[62],"We":[63,139],"focus":[64],"on":[65,121],"three":[66],"key":[67],"optimizations:":[68],"1)":[69],"Reordering":[70],"data":[72,89,104],"flow":[73],"scoring":[76],"algorithm":[77],"to":[78,87,102,135],"maximize":[79],"parallelism.":[80],"2)":[81],"Introducing":[82],"coarse-grained":[84],"batch-processing":[85],"strategy":[86,101],"enhance":[88],"reuse":[90],"hide":[92],"computation":[93],"latency.":[94],"3)":[95],"Implementing":[96],"hierarchical":[98],"memory":[99],"access":[100],"optimize":[103],"transfer":[105],"between":[106],"software":[107,137],"hardware.":[109],"Finally,":[110],"build":[112],"with":[116],"multi-threading":[117],"implement":[119],"it":[120],"Intel":[122],"Arria10":[123],"GX1150":[124],"FPGA.":[125],"Our":[126],"experimental":[127],"results":[128],"demonstrate":[129],"significant":[131],"improvement":[133],"compared":[134],"baseline.":[138],"achieve":[140],"7.23":[142],"times":[143,156],"speed-up":[144,157],"scoring,":[148],"while":[149],"complete":[151],"achieves":[153],"1.25":[155],"without":[158],"any":[159],"loss":[160],"accuracy.":[162]},"counts_by_year":[],"updated_date":"2025-12-21T23:12:01.093139","created_date":"2025-10-10T00:00:00"}