{"id":"https://openalex.org/W4292952490","doi":"https://doi.org/10.48550/arxiv.2208.09985","title":"Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs","display_name":"Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs","publication_year":2022,"publication_date":"2022-08-21","ids":{"openalex":"https://openalex.org/W4292952490","doi":"https://doi.org/10.48550/arxiv.2208.09985"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2208.09985","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2208.09985","pdf_url":"https://arxiv.org/pdf/2208.09985","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2208.09985","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042072020","display_name":"Jo\u00ebl Lindegger","orcid":"https://orcid.org/0000-0003-2581-8637"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Lindegger, Jo\u00ebl","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026337594","display_name":"Damla Senol Cali","orcid":"https://orcid.org/0000-0002-3665-6285"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cali, Damla Senol","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081055664","display_name":"Mohammed Alser","orcid":"https://orcid.org/0000-0002-6117-3701"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alser, Mohammed","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044416322","display_name":"Juan G\u00f3mez-Luna","orcid":"https://orcid.org/0000-0002-6514-1571"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"G\u00f3mez-Luna, Juan","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048764555","display_name":"Nika Mansouri Ghiasi","orcid":"https://orcid.org/0000-0002-0833-0042"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ghiasi, Nika Mansouri","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5050695684","display_name":"Onur Mutlu","orcid":"https://orcid.org/0000-0002-0075-2312"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mutlu, Onur","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5042072020"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.9995999932289124,"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":0.9995999932289124,"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":0.998199999332428,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9707000255584717,"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":0.8340814113616943},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.8222970366477966},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7333780527114868},{"id":"https://openalex.org/keywords/application-specific-integrated-circuit","display_name":"Application-specific integrated circuit","score":0.6666468381881714},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.6527495980262756},{"id":"https://openalex.org/keywords/memory-footprint","display_name":"Memory footprint","score":0.59902024269104},{"id":"https://openalex.org/keywords/footprint","display_name":"Footprint","score":0.5123494863510132},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.475132018327713},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.4460429549217224},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.28609445691108704},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09507367014884949}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8340814113616943},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.8222970366477966},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7333780527114868},{"id":"https://openalex.org/C77390884","wikidata":"https://www.wikidata.org/wiki/Q217302","display_name":"Application-specific integrated circuit","level":2,"score":0.6666468381881714},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.6527495980262756},{"id":"https://openalex.org/C74912251","wikidata":"https://www.wikidata.org/wiki/Q6815727","display_name":"Memory footprint","level":2,"score":0.59902024269104},{"id":"https://openalex.org/C132943942","wikidata":"https://www.wikidata.org/wiki/Q2562511","display_name":"Footprint","level":2,"score":0.5123494863510132},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.475132018327713},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.4460429549217224},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.28609445691108704},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09507367014884949},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2208.09985","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2208.09985","pdf_url":"https://arxiv.org/pdf/2208.09985","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2208.09985","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2208.09985","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2208.09985","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2208.09985","pdf_url":"https://arxiv.org/pdf/2208.09985","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2013643406","https://openalex.org/W4221139464","https://openalex.org/W4289827464","https://openalex.org/W3137434606","https://openalex.org/W4372263373"],"abstract_inverted_index":{"Pairwise":[0],"sequence":[1,72],"alignment":[2],"is":[3,31],"a":[4,49,55,67,127,137,149,167,191],"very":[5],"time-consuming":[6],"step":[7,15],"in":[8,43,92],"common":[9],"bioinformatics":[10],"pipelines.":[11],"Speeding":[12],"up":[13],"this":[14],"requires":[16],"heuristics,":[17],"efficient":[18,98],"implementations,":[19],"and/or":[20],"hardware":[21],"acceleration.":[22],"A":[23],"promising":[24],"candidate":[25],"for":[26,105],"all":[27],"of":[28,52,90,101,114,124,140,146,161,170,178,208,219,236],"the":[29,32,44,82,88,93,102,111,121,158,196,203,216,223],"above":[30],"recently":[33],"proposed":[34],"GenASM":[35,45,94,192,209],"algorithm.":[36,95],"We":[37,64,96,173],"identify":[38],"and":[39,59,69,87,107,130,136,154,166,186,205,210],"address":[40],"three":[41,76],"inefficiencies":[42],"algorithm:":[46],"it":[47],"has":[48],"high":[50],"amount":[51],"data":[53,83],"movement,":[54,84],"large":[56],"memory":[57,85],"footprint,":[58,86],"does":[60],"some":[61],"unnecessary":[62],"work.":[63],"propose":[65],"Scrooge,":[66,162],"fast":[68],"memory-frugal":[70],"genomic":[71],"aligner.":[73],"Scrooge":[74,103,125,147,179,211,220],"includes":[75],"novel":[77],"algorithmic":[78,116],"improvements":[79],"which":[80,109],"reduce":[81],"number":[89],"operations":[91],"provide":[97],"open-source":[99],"implementations":[100,235],"algorithm":[104],"CPUs":[106],"GPUs,":[108],"demonstrate":[110],"significant":[112],"benefits":[113],"our":[115],"improvements.":[117],"For":[118],"long":[119],"reads,":[120],"CPU":[122,138,159],"version":[123,145,160],"achieves":[126,148],"20.1x,":[128],"1.7x,":[129],"2.1x":[131,187],"speedup":[132,156],"over":[133,157],"KSW2,":[134,163],"Edlib,":[135,164],"implementation":[139,169,177],"GenASM,":[141,171],"respectively.":[142,172],"The":[143],"GPU":[144,168],"4.0x":[150],"80.4x,":[151],"6.8x,":[152],"12.6x":[153],"5.9x":[155],"Darwin-GPU,":[165],"estimate":[174],"an":[175],"ASIC":[176,193],"to":[180],"use":[181],"3.6x":[182],"less":[183,188],"chip":[184],"area":[185],"power":[189],"than":[190],"while":[194],"maintaining":[195],"same":[197],"throughput.":[198],"Further,":[199],"we":[200,226],"systematically":[201],"analyze":[202],"throughput":[204],"accuracy":[206],"behavior":[207],"under":[212],"various":[213],"configurations.":[214],"As":[215],"best":[217],"configuration":[218],"depends":[221],"on":[222],"computing":[224],"platform,":[225],"make":[227],"several":[228],"observations":[229],"that":[230],"can":[231],"help":[232],"guide":[233],"future":[234],"Scrooge.":[237],"Availability:":[238],"https://github.com/CMU-SAFARI/Scrooge":[239]},"counts_by_year":[],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
