{"id":"https://openalex.org/W4309264686","doi":"https://doi.org/10.1109/biocas54905.2022.9948621","title":"FAST: FPGA-based Acceleration of Genomic Sequence Trimming","display_name":"FAST: FPGA-based Acceleration of Genomic Sequence Trimming","publication_year":2022,"publication_date":"2022-10-13","ids":{"openalex":"https://openalex.org/W4309264686","doi":"https://doi.org/10.1109/biocas54905.2022.9948621"},"language":"en","primary_location":{"id":"doi:10.1109/biocas54905.2022.9948621","is_oa":false,"landing_page_url":"https://doi.org/10.1109/biocas54905.2022.9948621","pdf_url":null,"source":{"id":"https://openalex.org/S4363608179","display_name":"2022 IEEE Biomedical Circuits and Systems Conference (BioCAS)","issn_l":null,"issn":null,"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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE Biomedical Circuits and Systems Conference (BioCAS)","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,CSE Department,La Jolla,CA,USA,92093"],"affiliations":[{"raw_affiliation_string":"UC San Diego,CSE 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,CSE Department,La Jolla,CA,USA,92093"],"affiliations":[{"raw_affiliation_string":"UC San Diego,CSE Department,La Jolla,CA,USA,92093","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006769475","display_name":"Niya Shao","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":"Niya Shao","raw_affiliation_strings":["UC San Diego,CSE Department,La Jolla,CA,USA,92093"],"affiliations":[{"raw_affiliation_string":"UC San Diego,CSE 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/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,CSE Department,La Jolla,CA,USA,92093"],"affiliations":[{"raw_affiliation_string":"UC San Diego,CSE 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,CSE Department,La Jolla,CA,USA,92093"],"affiliations":[{"raw_affiliation_string":"UC San Diego,CSE Department,La Jolla,CA,USA,92093","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5060490428"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":null,"apc_paid":null,"fwci":0.8821,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.72310127,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"510","last_page":"514"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9994000196456909,"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":0.993399977684021,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9922000169754028,"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":0.7599503993988037},{"id":"https://openalex.org/keywords/trimming","display_name":"Trimming","score":0.7430068850517273},{"id":"https://openalex.org/keywords/adapter","display_name":"Adapter (computing)","score":0.6989235877990723},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.646415114402771},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6170016527175903},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.45884713530540466},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.4338158369064331},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.43047183752059937},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3861461281776428},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.29154330492019653},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19153746962547302},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.17113721370697021},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.12745150923728943},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08531409502029419}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7599503993988037},{"id":"https://openalex.org/C56951928","wikidata":"https://www.wikidata.org/wiki/Q3539213","display_name":"Trimming","level":2,"score":0.7430068850517273},{"id":"https://openalex.org/C177284502","wikidata":"https://www.wikidata.org/wiki/Q1005390","display_name":"Adapter (computing)","level":2,"score":0.6989235877990723},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.646415114402771},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6170016527175903},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.45884713530540466},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.4338158369064331},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.43047183752059937},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3861461281776428},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.29154330492019653},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19153746962547302},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.17113721370697021},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.12745150923728943},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08531409502029419},{"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/biocas54905.2022.9948621","is_oa":false,"landing_page_url":"https://doi.org/10.1109/biocas54905.2022.9948621","pdf_url":null,"source":{"id":"https://openalex.org/S4363608179","display_name":"2022 IEEE Biomedical Circuits and Systems Conference (BioCAS)","issn_l":null,"issn":null,"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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE Biomedical Circuits and Systems Conference (BioCAS)","raw_type":"proceedings-article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt0jn050w9","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/0jn050w9","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W2016853666","https://openalex.org/W2108234281","https://openalex.org/W2131271579","https://openalex.org/W2139437267","https://openalex.org/W2789843538","https://openalex.org/W2883847355","https://openalex.org/W2928905502","https://openalex.org/W2951912016","https://openalex.org/W2952946229","https://openalex.org/W2971801673","https://openalex.org/W3004986415","https://openalex.org/W3111214985","https://openalex.org/W3122491681","https://openalex.org/W4220962429","https://openalex.org/W6773649665"],"related_works":["https://openalex.org/W2467235537","https://openalex.org/W4243755427","https://openalex.org/W1493074871","https://openalex.org/W2222099502","https://openalex.org/W2128287377","https://openalex.org/W1979067309","https://openalex.org/W2375590729","https://openalex.org/W2385024427","https://openalex.org/W2978797270","https://openalex.org/W1972676838"],"abstract_inverted_index":{"The":[0,84],"sheer":[1],"amount":[2],"of":[3,70,93,124,145],"genomic":[4],"sequencing":[5],"data":[6,82],"generated":[7],"daily":[8],"that":[9,54],"requires":[10],"time-sensitive":[11],"processing":[12],"for":[13,17,122],"downstream":[14],"analysis":[15,126],"calls":[16],"accelerating":[18,27],"the":[19,28,32,44,52,98,136],"bioinformatics":[20],"pipelines.":[21],"Previous":[22],"studies":[23],"mainly":[24],"have":[25],"attempted":[26],"alignment":[29],"stage,":[30],"leaving":[31],"other":[33],"pipeline":[34],"stages":[35,53],"as":[36],"performance":[37],"bottlenecks.":[38],"In":[39],"this":[40],"work,":[41],"we":[42],"propose":[43],"first":[45],"FPGA-based":[46],"framework":[47,86],"dubbed":[48],"FAST":[49,65,128],"to":[50,75,131],"accelerate":[51],"deal":[55],"with":[56,107,116,139],"sequence":[57],"trimming,":[58],"in":[59,134],"particular":[60],"adapter":[61,101],"and":[62,72,90],"primer":[63],"removal.":[64],"supports":[66,91],"a":[67,140],"comprehensive":[68],"set":[69],"functionalities":[71],"is":[73,87],"convenient":[74],"use":[76],"by":[77,104],"operating":[78],"on":[79],"standard":[80],"genomics":[81],"formats.":[83],"proposed":[85],"fully":[88],"configurable":[89],"variety":[92],"runtime":[94],"settings.":[95],"It":[96],"surpasses":[97],"state-of-the-art":[99],"widely-used":[100],"trimmer":[102],"(fastp)":[103],"4.7\u00d7\u201329.4\u00d7":[105],"speed-up,":[106],"10.1\u00d7\u201354.9":[108],"less":[109],"energy,":[110],"respectively.":[111],"For":[112],"clipping":[113],"primers,":[114],"which":[115],"current":[117],"existing":[118],"tool":[119],"(iVar)":[120],"accounts":[121],"\u223c50%":[123],"SARS-CoV-2":[125],"pipeline,":[127],"achieves":[129],"up":[130],"62\u00d7":[132],"speed-up":[133],"trimming":[135],"virus":[137],"sequences":[138],"low":[141],"FPGA":[142],"resource":[143],"utilization":[144],"12%.":[146]},"counts_by_year":[{"year":2025,"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"}