{"id":"https://openalex.org/W4280508214","doi":"https://doi.org/10.1093/bioinformatics/btac333","title":"CURC: a CUDA-based reference-free read compressor","display_name":"CURC: a CUDA-based reference-free read compressor","publication_year":2022,"publication_date":"2022-05-17","ids":{"openalex":"https://openalex.org/W4280508214","doi":"https://doi.org/10.1093/bioinformatics/btac333","pmid":"https://pubmed.ncbi.nlm.nih.gov/35579371"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac333","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac333","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/12/3294/49885142/btac333.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/12/3294/49885142/btac333.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021288733","display_name":"Shaohui Xie","orcid":"https://orcid.org/0009-0007-5611-8066"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shaohui Xie","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University , Shenzhen 518060, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen 518060, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102481117","display_name":"Xiaotian He","orcid":null},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaotian He","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University , Shenzhen 518060, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen 518060, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068660482","display_name":"Shan He","orcid":"https://orcid.org/0000-0001-7117-1438"},"institutions":[{"id":"https://openalex.org/I79619799","display_name":"University of Birmingham","ror":"https://ror.org/03angcq70","country_code":"GB","type":"education","lineage":["https://openalex.org/I79619799"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shan He","raw_affiliation_strings":["School of Computer Science, University of Birmingham , Birmingham B15 2TT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, University of Birmingham , Birmingham B15 2TT, UK","institution_ids":["https://openalex.org/I79619799"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052762681","display_name":"Zexuan Zhu","orcid":"https://orcid.org/0000-0001-8479-6904"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zexuan Zhu","raw_affiliation_strings":["BGI-Shenzhen , Shenzhen 518083, China","College of Computer Science and Software Engineering, Shenzhen University , Shenzhen 518060, China"],"raw_orcid":"https://orcid.org/0000-0001-8479-6904","affiliations":[{"raw_affiliation_string":"BGI-Shenzhen , Shenzhen 518083, China","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen 518060, China","institution_ids":["https://openalex.org/I180726961"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5052762681"],"corresponding_institution_ids":["https://openalex.org/I100135526","https://openalex.org/I180726961"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0497,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.79969022,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"38","issue":"12","first_page":"3294","last_page":"3296"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.8529999852180481,"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":0.8529999852180481,"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":0.04580000042915344,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.017000000923871994,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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":0.8540270328521729},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.7825493812561035},{"id":"https://openalex.org/keywords/lossless-compression","display_name":"Lossless compression","score":0.7196598052978516},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.5791231393814087},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5385993123054504},{"id":"https://openalex.org/keywords/data-compression","display_name":"Data compression","score":0.5263389945030212},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.5144167542457581},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.50010085105896},{"id":"https://openalex.org/keywords/central-processing-unit","display_name":"Central processing unit","score":0.4450944662094116},{"id":"https://openalex.org/keywords/compression","display_name":"Compression (physics)","score":0.41970324516296387},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.2940884530544281},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.21227940917015076},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.16170546412467957}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8540270328521729},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.7825493812561035},{"id":"https://openalex.org/C81081738","wikidata":"https://www.wikidata.org/wiki/Q55542","display_name":"Lossless compression","level":3,"score":0.7196598052978516},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.5791231393814087},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5385993123054504},{"id":"https://openalex.org/C78548338","wikidata":"https://www.wikidata.org/wiki/Q2493","display_name":"Data compression","level":2,"score":0.5263389945030212},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.5144167542457581},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.50010085105896},{"id":"https://openalex.org/C49154492","wikidata":"https://www.wikidata.org/wiki/Q5300","display_name":"Central processing unit","level":2,"score":0.4450944662094116},{"id":"https://openalex.org/C180016635","wikidata":"https://www.wikidata.org/wiki/Q2712821","display_name":"Compression (physics)","level":2,"score":0.41970324516296387},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.2940884530544281},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.21227940917015076},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.16170546412467957},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0}],"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":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac333","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac333","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/12/3294/49885142/btac333.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35579371","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35579371","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac333","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac333","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/12/3294/49885142/btac333.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.4399999976158142,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G2840727465","display_name":"\u57fa\u4e8e\u81ea\u7ec4\u88c5\u53c2\u8003\u57fa\u56e0\u7ec4\u7684\u9ad8\u901a\u91cf\u957f\u8bfb\u6d4b\u5e8f\u6570\u636e\u538b\u7f29\u548c\u6bd4\u5bf9\u96c6\u6210\u7814\u7a76","funder_award_id":"61871272","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7560726216","display_name":null,"funder_award_id":"JCYJ20190808173617147","funder_id":"https://openalex.org/F4320329791","funder_display_name":"Shenzhen Fundamental Research Program"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320329791","display_name":"Shenzhen Fundamental Research Program","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4280508214.pdf","grobid_xml":"https://content.openalex.org/works/W4280508214.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2538355508","https://openalex.org/W2764165465","https://openalex.org/W2899544675","https://openalex.org/W2905575949","https://openalex.org/W2963360182","https://openalex.org/W2994713233","https://openalex.org/W3185657184"],"related_works":["https://openalex.org/W2983282793","https://openalex.org/W2020279179","https://openalex.org/W2503137108","https://openalex.org/W2119534391","https://openalex.org/W1966576946","https://openalex.org/W2023770367","https://openalex.org/W2062253548","https://openalex.org/W2393490604","https://openalex.org/W2393707426","https://openalex.org/W2146871484"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"data":[2,13,63,140],"deluge":[3],"of":[4,30,56,72,99,114],"high-throughput":[5],"sequencing":[6,62],"(HTS)":[7],"has":[8],"posed":[9],"great":[10],"challenges":[11],"to":[12,24,48,67],"storage":[14],"and":[15,46,107],"transfer.":[16],"Many":[17],"specific":[18],"compression":[19,98,116,119],"tools":[20],"have":[21],"been":[22],"developed":[23],"solve":[25],"this":[26],"problem.":[27],"However,":[28],"most":[29],"the":[31,54,69,104,115],"existing":[32],"compressors":[33,64],"are":[34,141],"based":[35,102],"on":[36,103],"central":[37],"processing":[38,58],"unit":[39],"(CPU)":[40],"platform,":[41],"which":[42],"might":[43],"be":[44,133],"inefficient":[45],"expensive":[47],"handle":[49],"large-scale":[50],"HTS":[51],"data.":[52],"With":[53],"popularization":[55],"graphics":[57],"units":[59],"(GPUs),":[60],"GPU-compatible":[61],"become":[65],"desirable":[66],"exploit":[68],"computing":[70],"power":[71],"GPUs.":[73],"RESULTS:":[74],"We":[75],"present":[76],"a":[77,88],"GPU-accelerated":[78],"reference-free":[79,125],"read":[80,126],"compressor,":[81],"namely":[82],"CURC,":[83],"for":[84],"FASTQ":[85],"files.":[86],"Under":[87],"GPU-CPU":[89],"heterogeneous":[90],"parallel":[91],"scheme,":[92],"CURC":[93,110,131],"implements":[94],"highly":[95],"efficient":[96],"lossless":[97],"DNA":[100],"stream":[101],"pseudogenome":[105],"approach":[106],"CUDA":[108],"library.":[109],"achieves":[111],"2-6-fold":[112],"speedup":[113],"with":[117,122],"competitive":[118],"rate,":[120],"compared":[121],"other":[123],"state-of-the-art":[124],"compressors.":[127],"AVAILABILITY":[128],"AND":[129],"IMPLEMENTATION:":[130],"can":[132],"downloaded":[134],"from":[135],"https://github.com/BioinfoSZU/CURC.":[136],"SUPPLEMENTARY":[137],"INFORMATION:":[138],"Supplementary":[139],"available":[142],"at":[143],"Bioinformatics":[144],"online.":[145]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}