{"id":"https://openalex.org/W4311839914","doi":"https://doi.org/10.1109/icfpt56656.2022.9974548","title":"SALIENT: Ultra-Fast FPGA-based Short Read Alignment","display_name":"SALIENT: Ultra-Fast FPGA-based Short Read Alignment","publication_year":2022,"publication_date":"2022-12-05","ids":{"openalex":"https://openalex.org/W4311839914","doi":"https://doi.org/10.1109/icfpt56656.2022.9974548"},"language":"en","primary_location":{"id":"doi:10.1109/icfpt56656.2022.9974548","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icfpt56656.2022.9974548","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 International Conference on Field-Programmable Technology (ICFPT)","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/A5060490428","display_name":"Behnam Khaleghi","orcid":"https://orcid.org/0000-0002-3655-0501"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Behnam Khaleghi","raw_affiliation_strings":["UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093"],"affiliations":[{"raw_affiliation_string":"UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100425396","display_name":"Tianqi Zhang","orcid":"https://orcid.org/0000-0003-3581-6184"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tianqi Zhang","raw_affiliation_strings":["UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093"],"affiliations":[{"raw_affiliation_string":"UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067810319","display_name":"Cameron Martino","orcid":"https://orcid.org/0000-0001-9334-1258"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cameron Martino","raw_affiliation_strings":["UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093"],"affiliations":[{"raw_affiliation_string":"UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000137125","display_name":"George Armstrong","orcid":"https://orcid.org/0000-0002-1061-3295"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"George Armstrong","raw_affiliation_strings":["UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093"],"affiliations":[{"raw_affiliation_string":"UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053738881","display_name":"Ameen Akel","orcid":null},"institutions":[{"id":"https://openalex.org/I11912373","display_name":"Micron (United States)","ror":"https://ror.org/02fv52296","country_code":"US","type":"company","lineage":["https://openalex.org/I11912373"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ameen Akel","raw_affiliation_strings":["Micron Technology, Inc"],"affiliations":[{"raw_affiliation_string":"Micron Technology, Inc","institution_ids":["https://openalex.org/I11912373"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043295211","display_name":"Ken Curewitz","orcid":null},"institutions":[{"id":"https://openalex.org/I11912373","display_name":"Micron (United States)","ror":"https://ror.org/02fv52296","country_code":"US","type":"company","lineage":["https://openalex.org/I11912373"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ken Curewitz","raw_affiliation_strings":["Micron Technology, Inc"],"affiliations":[{"raw_affiliation_string":"Micron Technology, Inc","institution_ids":["https://openalex.org/I11912373"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083516627","display_name":"Justin Eno","orcid":null},"institutions":[{"id":"https://openalex.org/I11912373","display_name":"Micron (United States)","ror":"https://ror.org/02fv52296","country_code":"US","type":"company","lineage":["https://openalex.org/I11912373"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Justin Eno","raw_affiliation_strings":["Micron Technology, Inc"],"affiliations":[{"raw_affiliation_string":"Micron Technology, Inc","institution_ids":["https://openalex.org/I11912373"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012522420","display_name":"Sean Eilert","orcid":"https://orcid.org/0000-0002-5378-2961"},"institutions":[{"id":"https://openalex.org/I11912373","display_name":"Micron (United States)","ror":"https://ror.org/02fv52296","country_code":"US","type":"company","lineage":["https://openalex.org/I11912373"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sean Eilert","raw_affiliation_strings":["Micron Technology, Inc"],"affiliations":[{"raw_affiliation_string":"Micron Technology, Inc","institution_ids":["https://openalex.org/I11912373"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033881627","display_name":"Rob Knight","orcid":"https://orcid.org/0000-0002-0975-9019"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rob Knight","raw_affiliation_strings":["UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093"],"affiliations":[{"raw_affiliation_string":"UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008998282","display_name":"Niema Moshiri","orcid":"https://orcid.org/0000-0003-2209-8128"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Niema Moshiri","raw_affiliation_strings":["UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093"],"affiliations":[{"raw_affiliation_string":"UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112841571","display_name":"Tajana Rosing","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tajana Rosing","raw_affiliation_strings":["UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093"],"affiliations":[{"raw_affiliation_string":"UC San Diego,Computer Science and Engineering Department,La Jolla,CA,USA,92093","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5060490428"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":null,"apc_paid":null,"fwci":0.3431,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.56306506,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9839000105857849,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9824000000953674,"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":0.8649033308029175},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.7195712924003601},{"id":"https://openalex.org/keywords/salient","display_name":"Salient","score":0.7171461582183838},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6851692795753479},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.6438074707984924},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.5962304472923279},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.538374125957489},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.43688642978668213},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.3486271798610687},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17235174775123596},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11409339308738708}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8649033308029175},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.7195712924003601},{"id":"https://openalex.org/C2780719617","wikidata":"https://www.wikidata.org/wiki/Q1030752","display_name":"Salient","level":2,"score":0.7171461582183838},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6851692795753479},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.6438074707984924},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.5962304472923279},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.538374125957489},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.43688642978668213},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.3486271798610687},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17235174775123596},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11409339308738708},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/icfpt56656.2022.9974548","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icfpt56656.2022.9974548","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 International Conference on Field-Programmable Technology (ICFPT)","raw_type":"proceedings-article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt0b95z7pw","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/0b95z7pw","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.41999998688697815}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1988651200","https://openalex.org/W1996753938","https://openalex.org/W1997446138","https://openalex.org/W2011175593","https://openalex.org/W2016853666","https://openalex.org/W2037113830","https://openalex.org/W2087064593","https://openalex.org/W2103441770","https://openalex.org/W2104846587","https://openalex.org/W2111305378","https://openalex.org/W2124985265","https://openalex.org/W2139814676","https://openalex.org/W2146496959","https://openalex.org/W2161556727","https://openalex.org/W2170551349","https://openalex.org/W2330100020","https://openalex.org/W2466826145","https://openalex.org/W2749499006","https://openalex.org/W2761496944","https://openalex.org/W2789843538","https://openalex.org/W2985670337","https://openalex.org/W3004986415","https://openalex.org/W3111214985","https://openalex.org/W3131193791","https://openalex.org/W3160765884","https://openalex.org/W4220962429","https://openalex.org/W4220983285","https://openalex.org/W4293196852","https://openalex.org/W6773649665","https://openalex.org/W6842402754"],"related_works":["https://openalex.org/W4380433113","https://openalex.org/W4386072068","https://openalex.org/W252339960","https://openalex.org/W2390529043","https://openalex.org/W2378320433","https://openalex.org/W2358343511","https://openalex.org/W2051877971","https://openalex.org/W1970117064","https://openalex.org/W1787170397","https://openalex.org/W4292347844"],"abstract_inverted_index":{"State-of-the-art":[0],"high-throughput":[1],"DNA":[2],"sequencers":[3],"output":[4],"terabytes":[5],"of":[6,33,38,68,78,118,139,177],"short":[7],"reads":[8,140],"that":[9,141,163],"typically":[10,27],"need":[11,142],"to":[12,15,21,42,143,193,212,226],"be":[13],"aligned":[14],"a":[16,36,66,75,115,137,167,197],"reference":[17],"genome":[18],"in":[19,45],"order":[20],"perform":[22],"downstream":[23],"analyses.":[24],"Because":[25],"alignment":[26,56,69,73,92,103,151,205],"dominates":[28],"the":[29,55,59,90,122,127,131,182,213,227],"total":[30],"run":[31],"time":[32],"bioinformatics":[34,124],"pipelines,":[35],"number":[37,77,117],"recent":[39],"work":[40],"sought":[41],"accelerate":[43],"it":[44,232],"hardware.":[46],"However,":[47],"existing":[48,91,214],"FPGA":[49,60,100,216],"implemen-tations":[50],"did":[51],"not":[52],"fully":[53],"optimize":[54],"algorithms":[57],"for":[58,99],"hardware":[61],"and":[62,94,96,126,189,206],"mainly":[63],"focused":[64],"on":[65,121,166],"subset":[67],"problems,":[70],"e.g.,":[71],"ungapped":[72,111,132,215],"with":[74,196],"limited":[76],"mismatches,":[79],"which":[80,113],"hinder":[81],"their":[82],"practical":[83],"utility.":[84],"In":[85],"this":[86],"work,":[87],"we":[88],"analyze":[89],"methods":[93],"identify":[95],"leverage":[97],"opportunities":[98],"acceleration.":[101],"Our":[102],"framework,":[104],"SALIENT,":[105,164],"first":[106],"carries":[107],"out":[108],"an":[109,174],"ultra-fast":[110],"alignment,":[112],"supports":[114],"flexible":[116],"mismatches.":[119],"Based":[120],"underlying":[123],"pipeline":[125],"information":[128],"provided":[129],"by":[130,187,191],"aligner,":[133,148],"SALIENT":[134,156,219,237],"then":[135],"identifies":[136],"fraction":[138],"go":[144],"through":[145],"its":[146],"gapped":[147,228],"thus":[149],"improving":[150],"throughput.":[152],"We":[153],"extensively":[154],"evaluate":[155],"using":[157],"diverse":[158],"datasets.":[159],"Experimental":[160],"results":[161],"indicate":[162],"running":[165],"single":[168],"Xilinx":[169],"Alveo":[170],"U280":[171],"device,":[172],"delivers":[173],"average":[175],"throughput":[176,242],"546":[178],"million":[179],"bases/second,":[180],"outperforming":[181],"state-":[183],"of-the-art":[184],"minimap2":[185],"software":[186],"40x,":[188],"Bowtie2":[190],"up":[192],"107":[194],"x,":[195],"similar":[198],"or":[199],"slightly":[200],"better":[201],"(~O.l":[202],"%-0.5":[203],"%)":[204],"error":[207],"(false":[208],"negative/positive)":[209],"rate.":[210],"Compared":[211],"aligners":[217,229],"[1]\u2013[4],":[218],"has":[220],"9.4-18x":[221],"higher":[222,241],"throughput/Watt,":[223],"while":[224],"compared":[225],"[5],":[230],"[6],":[231],"is":[233],"28\u201335":[234],"x":[235,240],"better.":[236],"achieves":[238],"7.6":[239],"than":[243],"Illumina":[244],"DRAGEN":[245],"Bio-IT":[246],"Platform":[247],"[7].":[248]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
