{"id":"https://openalex.org/W2576765647","doi":"https://doi.org/10.1109/samos.2016.7818334","title":"AccuRA: Accurate alignment of short reads on scalable reconfigurable accelerators","display_name":"AccuRA: Accurate alignment of short reads on scalable reconfigurable accelerators","publication_year":2016,"publication_date":"2016-07-01","ids":{"openalex":"https://openalex.org/W2576765647","doi":"https://doi.org/10.1109/samos.2016.7818334","mag":"2576765647"},"language":"en","primary_location":{"id":"doi:10.1109/samos.2016.7818334","is_oa":false,"landing_page_url":"https://doi.org/10.1109/samos.2016.7818334","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 International Conference on Embedded Computer Systems: Architectures, Modeling and Simulation (SAMOS)","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/A5091343825","display_name":"Santhi Natarajan","orcid":"https://orcid.org/0000-0002-6701-826X"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Santhi Natarajan","raw_affiliation_strings":["Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, India"],"affiliations":[{"raw_affiliation_string":"Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, India","institution_ids":["https://openalex.org/I59270414"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026988156","display_name":"Naveen Kumar","orcid":"https://orcid.org/0000-0002-4788-7599"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"N Krishna Kumar","raw_affiliation_strings":["Indian Institute of Science, Bangalore, Karnataka, IN"],"affiliations":[{"raw_affiliation_string":"Indian Institute of Science, Bangalore, Karnataka, IN","institution_ids":["https://openalex.org/I59270414"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026479756","display_name":"Debnath Pal","orcid":"https://orcid.org/0000-0002-3591-5978"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Debnath Pal","raw_affiliation_strings":["Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India","institution_ids":["https://openalex.org/I59270414"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112000841","display_name":"S. K. Nandy","orcid":null},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"S. K. Nandy","raw_affiliation_strings":["Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India","institution_ids":["https://openalex.org/I59270414"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5091343825"],"corresponding_institution_ids":["https://openalex.org/I59270414"],"apc_list":null,"apc_paid":null,"fwci":0.6972,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.75451262,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"79","last_page":"87"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.994700014591217,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental 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":0.7989295721054077},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7195566892623901},{"id":"https://openalex.org/keywords/firmware","display_name":"Firmware","score":0.6856165528297424},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5977287292480469},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.5294503569602966},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4802406430244446},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.4305160343647003},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.4268658459186554},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.29265573620796204},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.28103262186050415},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13761460781097412}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7989295721054077},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7195566892623901},{"id":"https://openalex.org/C67212190","wikidata":"https://www.wikidata.org/wiki/Q104851","display_name":"Firmware","level":2,"score":0.6856165528297424},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5977287292480469},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.5294503569602966},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4802406430244446},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.4305160343647003},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.4268658459186554},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.29265573620796204},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.28103262186050415},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13761460781097412},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"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/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/samos.2016.7818334","is_oa":false,"landing_page_url":"https://doi.org/10.1109/samos.2016.7818334","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 International Conference on Embedded Computer Systems: Architectures, Modeling and Simulation (SAMOS)","raw_type":"proceedings-article"},{"id":"pmh:oai:eprints.iisc.ac.in:56921","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4377196309","display_name":"NOT FOUND REPOSITORY (Indian Institute of Science Bangalore)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I59270414","host_organization_name":"Indian Institute of Science Bangalore","host_organization_lineage":["https://openalex.org/I59270414"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Conference Proceedings"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W121571527","https://openalex.org/W639550976","https://openalex.org/W1570617259","https://openalex.org/W1973530293","https://openalex.org/W1980397590","https://openalex.org/W1992440403","https://openalex.org/W1992519395","https://openalex.org/W2011175593","https://openalex.org/W2037113830","https://openalex.org/W2046220835","https://openalex.org/W2072763119","https://openalex.org/W2087064593","https://openalex.org/W2089610326","https://openalex.org/W2094519647","https://openalex.org/W2103441770","https://openalex.org/W2105821863","https://openalex.org/W2124985265","https://openalex.org/W2126992668","https://openalex.org/W2144316495","https://openalex.org/W2146496959","https://openalex.org/W6605010064","https://openalex.org/W6634241951","https://openalex.org/W6668594571"],"related_works":["https://openalex.org/W2582981600","https://openalex.org/W4389238932","https://openalex.org/W4387467152","https://openalex.org/W4212885212","https://openalex.org/W4379115910","https://openalex.org/W3010413952","https://openalex.org/W4253989935","https://openalex.org/W2810560948","https://openalex.org/W2070793896","https://openalex.org/W4206124993"],"abstract_inverted_index":{"Classified":[0],"as":[1],"a":[2,43,80,105,151],"big":[3],"data":[4,30],"problem,":[5],"Short":[6],"Read":[7],"Mapping":[8],"(SRM)":[9],"within":[10],"the":[11,26,115,137,195],"Next":[12],"Generation":[13],"Sequencing":[14],"(NGS)":[15],"pipeline":[16],"presents":[17],"profound":[18],"technical":[19],"and":[20,51,62,74,110,140],"computing":[21],"challenges.":[22],"Existing":[23],"solutions":[24],"handle":[25],"high":[27,84],"volume":[28],"of":[29,91,114,162,177,184],"leveraging":[31],"heuristics,":[32],"to":[33,67,194],"claim":[34],"notable":[35],"performance":[36,85,161],"standards.":[37],"The":[38,143],"results":[39,64],"from":[40,65,188],"SRM":[41,135],"leave":[42],"huge":[44],"impact":[45],"across":[46],"fields,":[47],"including":[48],"medical":[49],"diagnostics":[50],"drug":[52],"discovery.":[53],"In":[54],"this":[55],"context,":[56],"we":[57,77],"need":[58],"precise,":[59],"affordable,":[60],"reliable":[61],"actionable":[63],"SRM,":[66],"support":[68],"any":[69],"application,":[70],"with":[71,95,130,158],"uncompromised":[72],"accuracy":[73],"performance.":[75],"Here,":[76],"present":[78],"AccuRA,":[79],"massively":[81],"parallel,":[82],"scalable,":[83],"reconfigurable":[86,153],"accelerator":[87],"for":[88],"accurate":[89],"alignment":[90,160],"short":[92,102,156],"reads.":[93],"Supplemented":[94],"multithreaded":[96],"firmware":[97],"architecture,":[98],"AccuRA":[99,144,170],"precisely":[100],"aligns":[101,155],"reads,":[103],"at":[104,174],"fine-grained":[106],"single":[107,152],"nucleotide":[108],"resolution,":[109],"offers":[111],"full":[112],"coverage":[113],"genome.":[116,199],"AccuRA's":[117],"parallel":[118],"dynamic":[119],"programming":[120],"kernels":[121],"seamlessly":[122],"perform":[123],"traceback":[124],"process":[125],"in":[126,136],"hardware":[127],"simultaneously":[128],"along":[129],"forward":[131],"scan,":[132],"thus":[133],"achieving":[134],"minimum":[138],"possible":[139],"deterministic":[141],"time.":[142],"prototype,":[145],"hosting":[146],"eight":[147],"kernel":[148],"units":[149],"on":[150],"device,":[154],"reads":[157],"an":[159],"20.48":[163],"Giga":[164],"Cell":[165],"Updates":[166],"Per":[167],"Second":[168],"(GCUPs).":[169],"also":[171],"scales":[172],"well":[173],"multiple":[175],"levels":[176],"design":[178],"granularity,":[179],"while":[180],"successfully":[181],"aligning":[182],"genomes":[183],"various":[185],"sizes,":[186],"ranging":[187],"small":[189],"archeal,":[190],"bacterial,":[191],"fungal":[192],"genomes,":[193],"large":[196],"mammalian":[197],"human":[198]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
