{"id":"https://openalex.org/W3193826708","doi":"https://doi.org/10.1109/tcbb.2021.3106311","title":"An FPGA Based Energy-Efficient Read Mapper With Parallel Filtering and In-Situ Verification","display_name":"An FPGA Based Energy-Efficient Read Mapper With Parallel Filtering and In-Situ Verification","publication_year":2021,"publication_date":"2021-08-20","ids":{"openalex":"https://openalex.org/W3193826708","doi":"https://doi.org/10.1109/tcbb.2021.3106311","mag":"3193826708","pmid":"https://pubmed.ncbi.nlm.nih.gov/34415836"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3106311","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3106311","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5079401295","display_name":"Venkateshwarlu Y. Gudur","orcid":"https://orcid.org/0000-0002-6476-7222"},"institutions":[{"id":"https://openalex.org/I65181880","display_name":"Indian Institute of Technology Hyderabad","ror":"https://ror.org/01j4v3x97","country_code":"IN","type":"education","lineage":["https://openalex.org/I65181880"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Venkateshwarlu Yellaswamy Gudur","raw_affiliation_strings":["Department of Electrical Engineering, Indian Institute of Technology Hyderabad, Kandi, Telangana, India"],"raw_orcid":"https://orcid.org/0000-0002-6476-7222","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, Indian Institute of Technology Hyderabad, Kandi, Telangana, India","institution_ids":["https://openalex.org/I65181880"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061841041","display_name":"Sidharth Maheshwari","orcid":"https://orcid.org/0000-0002-9665-5698"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sidharth Maheshwari","raw_affiliation_strings":["School of Engineering, Newcastle University, Newcastle Upon Tyne, U.K"],"raw_orcid":"https://orcid.org/0000-0002-9665-5698","affiliations":[{"raw_affiliation_string":"School of Engineering, Newcastle University, Newcastle Upon Tyne, U.K","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044085104","display_name":"Amit Acharyya","orcid":"https://orcid.org/0000-0002-5636-0676"},"institutions":[{"id":"https://openalex.org/I65181880","display_name":"Indian Institute of Technology Hyderabad","ror":"https://ror.org/01j4v3x97","country_code":"IN","type":"education","lineage":["https://openalex.org/I65181880"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Amit Acharyya","raw_affiliation_strings":["Department of Electrical Engineering, Indian Institute of Technology Hyderabad, Kandi, Telangana, India"],"raw_orcid":"https://orcid.org/0000-0002-5636-0676","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, Indian Institute of Technology Hyderabad, Kandi, Telangana, India","institution_ids":["https://openalex.org/I65181880"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077777787","display_name":"Rishad Shafik","orcid":"https://orcid.org/0000-0001-5444-537X"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Rishad Shafik","raw_affiliation_strings":["School of Engineering, Newcastle University, Newcastle Upon Tyne, U.K"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Engineering, Newcastle University, Newcastle Upon Tyne, U.K","institution_ids":["https://openalex.org/I84884186"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1399,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.55651178,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"19","issue":"5","first_page":"2697","last_page":"2711"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9994000196456909,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9994000196456909,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9973000288009644,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9860000014305115,"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":0.7631158828735352},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.648396372795105},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.5682506561279297},{"id":"https://openalex.org/keywords/mpsoc","display_name":"MPSoC","score":0.5353015065193176},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4745909869670868},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4637376070022583},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.3960540294647217},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3719657063484192},{"id":"https://openalex.org/keywords/computer-engineering","display_name":"Computer engineering","score":0.36978524923324585},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.3569703698158264},{"id":"https://openalex.org/keywords/real-time-computing","display_name":"Real-time computing","score":0.3533654808998108},{"id":"https://openalex.org/keywords/system-on-a-chip","display_name":"System on a chip","score":0.2832488417625427},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10292184352874756}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7631158828735352},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.648396372795105},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.5682506561279297},{"id":"https://openalex.org/C2777187653","wikidata":"https://www.wikidata.org/wiki/Q975106","display_name":"MPSoC","level":3,"score":0.5353015065193176},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4745909869670868},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4637376070022583},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.3960540294647217},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3719657063484192},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.36978524923324585},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.3569703698158264},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.3533654808998108},{"id":"https://openalex.org/C118021083","wikidata":"https://www.wikidata.org/wiki/Q610398","display_name":"System on a chip","level":2,"score":0.2832488417625427},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10292184352874756}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbb.2021.3106311","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3106311","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34415836","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34415836","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:raiith.iith.ac.in:11034","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400292","display_name":"Research Archive of Indian Institute of Technology Hyderabad (Indian Institute of Technology Hyderabad)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I65181880","host_organization_name":"Indian Institute of Technology Hyderabad","host_organization_lineage":["https://openalex.org/I65181880"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:raiith.iith.ac.in:8958","is_oa":false,"landing_page_url":"http://raiith.iith.ac.in/8958/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400292","display_name":"Research Archive of Indian Institute of Technology Hyderabad (Indian Institute of Technology Hyderabad)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I65181880","host_organization_name":"Indian Institute of Technology Hyderabad","host_organization_lineage":["https://openalex.org/I65181880"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.6200000047683716}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320295","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W1498160656","https://openalex.org/W1534435001","https://openalex.org/W1577822803","https://openalex.org/W1848911929","https://openalex.org/W1979321046","https://openalex.org/W1998048394","https://openalex.org/W2011175593","https://openalex.org/W2014794755","https://openalex.org/W2025648894","https://openalex.org/W2028431438","https://openalex.org/W2028445324","https://openalex.org/W2034798008","https://openalex.org/W2052601433","https://openalex.org/W2082346787","https://openalex.org/W2084594458","https://openalex.org/W2093931624","https://openalex.org/W2098416496","https://openalex.org/W2100751585","https://openalex.org/W2104846587","https://openalex.org/W2110045923","https://openalex.org/W2121716038","https://openalex.org/W2131417499","https://openalex.org/W2133687564","https://openalex.org/W2139747296","https://openalex.org/W2140154634","https://openalex.org/W2142759233","https://openalex.org/W2146496959","https://openalex.org/W2147726041","https://openalex.org/W2154468535","https://openalex.org/W2156715753","https://openalex.org/W2156976066","https://openalex.org/W2157375578","https://openalex.org/W2168303240","https://openalex.org/W2168459716","https://openalex.org/W2170551349","https://openalex.org/W2171777347","https://openalex.org/W2177379918","https://openalex.org/W2262429236","https://openalex.org/W2330100020","https://openalex.org/W2381025376","https://openalex.org/W2433194246","https://openalex.org/W2560228154","https://openalex.org/W2585711475","https://openalex.org/W2587851098","https://openalex.org/W2728531063","https://openalex.org/W2761496944","https://openalex.org/W2766890412","https://openalex.org/W2770446264","https://openalex.org/W2790091177","https://openalex.org/W2901728847","https://openalex.org/W2903688928","https://openalex.org/W2976324826","https://openalex.org/W3046494740","https://openalex.org/W3101704407","https://openalex.org/W3103269557","https://openalex.org/W3105003914","https://openalex.org/W4247053599","https://openalex.org/W4254502766","https://openalex.org/W6681400327"],"related_works":["https://openalex.org/W2110564838","https://openalex.org/W55440466","https://openalex.org/W2374428661","https://openalex.org/W2945897719","https://openalex.org/W2390965452","https://openalex.org/W2095366957","https://openalex.org/W2393801835","https://openalex.org/W3095609119","https://openalex.org/W2384157887","https://openalex.org/W2528057492"],"abstract_inverted_index":{"In":[0],"the":[1,18,45,91,118,141,173],"assembly":[2],"pipeline":[3],"of":[4,33],"Whole":[5],"Genome":[6],"Sequencing":[7],"(WGS),":[8],"read":[9,77],"mapping":[10,78],"is":[11,88,107,123,148],"a":[12,30,40,80,97,110],"widely":[13],"used":[14],"method":[15,116],"to":[16,156,159,165],"re-assemble":[17],"genome.":[19],"It":[20,147],"employs":[21],"approximate":[22],"string":[23],"matching":[24],"and":[25,35,55,63,94,102,121,163,176],"dynamic":[26],"programming-based":[27],"algorithms":[28],"on":[29,90,140],"large":[31],"volume":[32],"data":[34,47,61,155],"associated":[36],"structures,":[37],"making":[38],"it":[39,122],"computationally":[41],"intensive":[42],"process.":[43],"Currently,":[44],"state-of-the-art":[46,174],"centers":[48],"for":[49,58,76,100,117],"genome":[50],"sequencing":[51],"incur":[52],"substantial":[53],"setup":[54],"energy":[56,161],"costs":[57],"maintaining":[59],"hardware,":[60],"storage":[62],"cooling":[64],"systems.":[65],"To":[66],"enable":[67],"low-cost":[68],"genomics,":[69],"we":[70],"propose":[71],"an":[72,126],"energy-efficient":[73],"architectural":[74],"methodology":[75,87],"using":[79,96,109,130,152],"single":[81],"system-on-chip":[82],"(SoC)":[83],"platform.":[84,146],"The":[85,104],"proposed":[86],"based":[89,115],"q-gram":[92,113],"lemma":[93,114],"designed":[95,108],"novel":[98],"architecture":[99],"filtering":[101,105],"verification.":[103],"algorithm":[106],"parallel":[111,131],"sorted":[112],"first":[119],"time,":[120],"complemented":[124],"by":[125],"in-situ":[127],"verification":[128],"routine":[129],"Myers":[132],"bit-vector":[133],"algorithm.":[134],"We":[135],"have":[136],"implemented":[137],"our":[138],"design":[139],"Zynq":[142],"Ultrascale+":[143],"XCZU9EG":[144],"MPSoC":[145],"then":[149],"extensively":[150],"validated":[151],"real":[153],"genomic":[154],"demonstrate":[157],"up":[158,164],"7.8\u00d7":[160],"reduction":[162],"13.3\u00d7":[166],"less":[167],"resource":[168],"utilization":[169],"when":[170],"compared":[171],"with":[172],"software":[175],"hardware":[177],"approaches.":[178]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
