{"id":"https://openalex.org/W2562227272","doi":"https://doi.org/10.1186/s12859-016-1434-6","title":"Accelerating metagenomic read classification on CUDA-enabled GPUs","display_name":"Accelerating metagenomic read classification on CUDA-enabled GPUs","publication_year":2017,"publication_date":"2017-01-03","ids":{"openalex":"https://openalex.org/W2562227272","doi":"https://doi.org/10.1186/s12859-016-1434-6","mag":"2562227272","pmid":"https://pubmed.ncbi.nlm.nih.gov/28049411"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-1434-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1434-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1434-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1434-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043372390","display_name":"Robin Kobus","orcid":"https://orcid.org/0000-0003-2726-1908"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Robin Kobus","raw_affiliation_strings":["Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany. rkobus@students.uni-mainz.de","Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany. rkobus@students.uni-mainz.de","institution_ids":[]},{"raw_affiliation_string":"Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027561629","display_name":"Christian Hundt","orcid":"https://orcid.org/0000-0002-7995-1858"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christian Hundt","raw_affiliation_strings":["Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107834032","display_name":"Andr\u00e9 C. M\u00fcller","orcid":"https://orcid.org/0000-0002-8312-5786"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andr\u00e9 M\u00fcller","raw_affiliation_strings":["Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bertil Schmidt","raw_affiliation_strings":["Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany","institution_ids":["https://openalex.org/I197323543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5043372390"],"corresponding_institution_ids":["https://openalex.org/I197323543"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5595,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.64973147,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"18","issue":"1","first_page":"11","last_page":"11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9886000156402588,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9858999848365784,"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/cuda","display_name":"CUDA","score":0.8443869352340698},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.8146907687187195},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7815369367599487},{"id":"https://openalex.org/keywords/titan","display_name":"Titan (rocket family)","score":0.5813455581665039},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.526881992816925},{"id":"https://openalex.org/keywords/workstation","display_name":"Workstation","score":0.49633604288101196},{"id":"https://openalex.org/keywords/xeon","display_name":"Xeon","score":0.47383102774620056},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.46812617778778076},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.4466198682785034},{"id":"https://openalex.org/keywords/xeon-phi","display_name":"Xeon Phi","score":0.43807563185691833},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.4194505512714386},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.31821364164352417},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.21616339683532715},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.17944681644439697},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.171290785074234}],"concepts":[{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.8443869352340698},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8146907687187195},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7815369367599487},{"id":"https://openalex.org/C50805821","wikidata":"https://www.wikidata.org/wiki/Q1136670","display_name":"Titan (rocket family)","level":2,"score":0.5813455581665039},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.526881992816925},{"id":"https://openalex.org/C67953723","wikidata":"https://www.wikidata.org/wiki/Q192525","display_name":"Workstation","level":2,"score":0.49633604288101196},{"id":"https://openalex.org/C145108525","wikidata":"https://www.wikidata.org/wiki/Q656154","display_name":"Xeon","level":2,"score":0.47383102774620056},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.46812617778778076},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.4466198682785034},{"id":"https://openalex.org/C96972482","wikidata":"https://www.wikidata.org/wiki/Q1049168","display_name":"Xeon Phi","level":2,"score":0.43807563185691833},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.4194505512714386},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31821364164352417},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21616339683532715},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.17944681644439697},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.171290785074234},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C87355193","wikidata":"https://www.wikidata.org/wiki/Q411","display_name":"Astrobiology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","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":3,"locations":[{"id":"doi:10.1186/s12859-016-1434-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1434-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1434-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28049411","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28049411","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5209836","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5209836","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-016-1434-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1434-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1434-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2562227272.pdf","grobid_xml":"https://content.openalex.org/works/W2562227272.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W2003347102","https://openalex.org/W2034937344","https://openalex.org/W2040486579","https://openalex.org/W2042417858","https://openalex.org/W2054226908","https://openalex.org/W2055043387","https://openalex.org/W2070102345","https://openalex.org/W2113601822","https://openalex.org/W2113679889","https://openalex.org/W2116895571","https://openalex.org/W2128124531","https://openalex.org/W2128769815","https://openalex.org/W2157539385","https://openalex.org/W2159954944","https://openalex.org/W2168477171","https://openalex.org/W2277827603","https://openalex.org/W2501688401","https://openalex.org/W2597444305","https://openalex.org/W2951176108","https://openalex.org/W2951214399","https://openalex.org/W2952465196"],"related_works":["https://openalex.org/W1974923383","https://openalex.org/W2739740241","https://openalex.org/W2475524688","https://openalex.org/W2085105049","https://openalex.org/W2148563915","https://openalex.org/W2526069705","https://openalex.org/W2019153376","https://openalex.org/W2024016913","https://openalex.org/W2981664121","https://openalex.org/W2796552083"],"abstract_inverted_index":{"cuCLARK":[0],"can":[1,20],"perform":[2],"metagenomic":[3],"read":[4],"classification":[5],"at":[6,23],"superior":[7],"speeds":[8],"on":[9],"CUDA-enabled":[10],"GPUs.":[11],"It":[12],"is":[13],"free":[14,25],"software":[15],"licensed":[16],"under":[17],"GPL":[18],"and":[19],"be":[21],"downloaded":[22],"https://github.com/funatiq/cuclark":[24],"of":[26],"charge.":[27]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
