{"id":"https://openalex.org/W2976324826","doi":"https://doi.org/10.1109/tcbb.2019.2943856","title":"CORAL: Verification-Aware OpenCL Based Read Mapper for Heterogeneous Systems","display_name":"CORAL: Verification-Aware OpenCL Based Read Mapper for Heterogeneous Systems","publication_year":2019,"publication_date":"2019-09-26","ids":{"openalex":"https://openalex.org/W2976324826","doi":"https://doi.org/10.1109/tcbb.2019.2943856","mag":"2976324826","pmid":"https://pubmed.ncbi.nlm.nih.gov/31562102"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2943856","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2943856","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/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":true,"raw_author_name":"Sidharth Maheshwari","raw_affiliation_strings":["School of Engineering, Newcastle University, Newcastle Upon Tyne, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Engineering, Newcastle University, Newcastle Upon Tyne, United Kingdom","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","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 Y. Gudur","raw_affiliation_strings":["Department of Electrical Engineering, Indian Institute of Technology (IIT), Hyderabad, Telangana, India"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, Indian Institute of Technology (IIT), Hyderabad, Telangana, India","institution_ids":["https://openalex.org/I65181880"]}]},{"author_position":"middle","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, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Engineering, Newcastle University, Newcastle Upon Tyne, United Kingdom","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045339285","display_name":"Ian Wilson","orcid":"https://orcid.org/0000-0001-6893-2873"},"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":"Ian Wilson","raw_affiliation_strings":["Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029446985","display_name":"Alex Yakovlev","orcid":"https://orcid.org/0000-0003-0826-9330"},"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":"Alex Yakovlev","raw_affiliation_strings":["School of Engineering, Newcastle University, Newcastle Upon Tyne, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Engineering, Newcastle University, Newcastle Upon Tyne, United Kingdom","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"last","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 (IIT), Hyderabad, Telangana, India"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, Indian Institute of Technology (IIT), Hyderabad, Telangana, India","institution_ids":["https://openalex.org/I65181880"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5061841041"],"corresponding_institution_ids":["https://openalex.org/I84884186"],"apc_list":null,"apc_paid":null,"fwci":0.3436,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.60011083,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"18","issue":"4","first_page":"1426","last_page":"1438"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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":0.9986000061035156,"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":0.9976000189781189,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9740999937057495,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.8626327514648438},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6358553171157837},{"id":"https://openalex.org/keywords/overhead","display_name":"Overhead (engineering)","score":0.5964338183403015},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.4900030195713043},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.48780301213264465},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.46985355019569397},{"id":"https://openalex.org/keywords/symmetric-multiprocessor-system","display_name":"Symmetric multiprocessor system","score":0.45140326023101807},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.45090028643608093},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.44494983553886414},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41739949584007263},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3847618103027344},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3317854404449463},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.3110666573047638},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19268634915351868},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.13887694478034973}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8626327514648438},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6358553171157837},{"id":"https://openalex.org/C2779960059","wikidata":"https://www.wikidata.org/wiki/Q7113681","display_name":"Overhead (engineering)","level":2,"score":0.5964338183403015},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.4900030195713043},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.48780301213264465},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.46985355019569397},{"id":"https://openalex.org/C172430144","wikidata":"https://www.wikidata.org/wiki/Q17111997","display_name":"Symmetric multiprocessor system","level":2,"score":0.45140326023101807},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.45090028643608093},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.44494983553886414},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41739949584007263},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3847618103027344},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3317854404449463},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.3110666573047638},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19268634915351868},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.13887694478034973}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2019.2943856","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2943856","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:31562102","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31562102","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:9019","is_oa":false,"landing_page_url":"https://ieeexplore.ieee.org/document/8850065/","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":[],"awards":[{"id":"https://openalex.org/G732396245","display_name":null,"funder_award_id":"EP/N023641/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7639885267","display_name":null,"funder_award_id":"EP/K034448/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W26356079","https://openalex.org/W642457968","https://openalex.org/W794840634","https://openalex.org/W1498160656","https://openalex.org/W1864199185","https://openalex.org/W2025648894","https://openalex.org/W2034798008","https://openalex.org/W2100751585","https://openalex.org/W2104846587","https://openalex.org/W2128016314","https://openalex.org/W2128120785","https://openalex.org/W2133687564","https://openalex.org/W2142759233","https://openalex.org/W2154468535","https://openalex.org/W2156715753","https://openalex.org/W2157375578","https://openalex.org/W2158322625","https://openalex.org/W2158874082","https://openalex.org/W2161488606","https://openalex.org/W2170551349","https://openalex.org/W2203839354","https://openalex.org/W2433194246","https://openalex.org/W2560228154","https://openalex.org/W2756215207","https://openalex.org/W2766890412","https://openalex.org/W2792005838","https://openalex.org/W2884212285","https://openalex.org/W2935576241","https://openalex.org/W3103269557","https://openalex.org/W4247053599","https://openalex.org/W6681400327","https://openalex.org/W6683504902"],"related_works":["https://openalex.org/W4360764256","https://openalex.org/W1784146144","https://openalex.org/W94000989","https://openalex.org/W2074226157","https://openalex.org/W3001194762","https://openalex.org/W2092071486","https://openalex.org/W4242263690","https://openalex.org/W3117765010","https://openalex.org/W1505993080","https://openalex.org/W3119609495"],"abstract_inverted_index":{"Genomics":[0],"has":[1],"the":[2,30,79,92,126,132,136,165,188,201,207],"potential":[3],"to":[4,9,65,101,120,131,191,194,198],"transform":[5],"medicine":[6],"from":[7],"reactive":[8],"a":[10,19,37,141,176],"personalized,":[11],"predictive,":[12],"preventive,":[13],"and":[14,57,63,75,228],"participatory":[15],"(P4)":[16],"form.":[17],"Being":[18],"Big":[20],"Data":[21],"application":[22],"with":[23,129,181,223],"continuously":[24],"increasing":[25],"rate":[26],"of":[27,33,47,50,95,135,151],"data":[28],"production,":[29],"computational":[31,93,160],"costs":[32],"genomics":[34],"have":[35],"become":[36],"daunting":[38],"challenge.":[39],"Most":[40],"modern":[41],"computing":[42,51],"systems":[43],"are":[44,110,203],"heterogeneous":[45,154],"consisting":[46],"various":[48],"combinations":[49],"resources,":[52],"such":[53,89],"as":[54],"CPUs,":[55],"GPUs,":[56,186],"FPGAs.":[58],"They":[59],"require":[60],"platform-specific":[61],"software":[62],"languages":[64],"program":[66],"making":[67],"their":[68],"simultaneous":[69],"operation":[70],"challenging.":[71],"Existing":[72],"read":[73],"mappers":[74,225],"analysis":[76],"tools":[77],"in":[78,115,221],"whole":[80],"genome":[81],"sequencing":[82],"(WGS)":[83],"pipeline":[84],"do":[85],"not":[86],"scale":[87],"for":[88],"heterogeneity.":[90],"Additionally,":[91],"cost":[94],"mapping":[96,133],"reads":[97],"is":[98,118,149,232],"high":[99],"due":[100],"expensive":[102],"dynamic":[103],"programming":[104,170],"based":[105],"verification,":[106],"where":[107],"optimized":[108],"implementations":[109],"already":[111],"available.":[112],"Thus,":[113],"improvement":[114],"filtration":[116],"techniques":[117],"needed":[119],"reduce":[121,159,206],"verification":[122,208],"overhead.":[123],"To":[124,205],"address":[125],"aforementioned":[127],"limitations":[128],"regards":[130],"element":[134],"WGS":[137],"pipeline,":[138],"we":[139],"propose":[140],"Cross-platfOrm":[142],"Read":[143],"mApper":[144],"using":[145,226],"opencL":[146],"(CORAL).":[147],"CORAL":[148,210,231],"capable":[150],"executing":[152],"on":[153,175],"devices/platforms,":[155],"simultaneously.":[156],"It":[157],"can":[158],"time":[161],"by":[162],"suitably":[163],"distributing":[164,187],"workload":[166,189],"without":[167],"any":[168],"additional":[169],"effort.":[171],"We":[172,217],"showcase":[173],"this":[174],"quadcore":[177],"Intel":[178],"CPU":[179],"along":[180],"two":[182],"Nvidia":[183],"GTX":[184],"590":[185],"judiciously":[190],"achieve":[192],"up":[193],"2\u00d7":[195],"speedup":[196],"compared":[197],"when,":[199],"only,":[200],"CPUs":[202],"used.":[204],"overhead,":[209],"dynamically":[211],"adapts":[212],"k-mer":[213],"length":[214],"during":[215],"filtration.":[216],"demonstrate":[218],"competitive":[219],"timings":[220],"comparison":[222],"other":[224],"real":[227],"simulated":[229],"reads.":[230],"available":[233],"at:":[234],"https://github.com/nclaes/CORAL.":[235]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
