{"id":"https://openalex.org/W2105868188","doi":"https://doi.org/10.1186/1471-2105-13-221","title":"ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data","display_name":"ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data","publication_year":2012,"publication_date":"2012-09-04","ids":{"openalex":"https://openalex.org/W2105868188","doi":"https://doi.org/10.1186/1471-2105-13-221","mag":"2105868188","pmid":"https://pubmed.ncbi.nlm.nih.gov/22946927"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-221","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-221","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-221","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/counter/pdf/10.1186/1471-2105-13-221","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049359065","display_name":"Christopher R. Cabanski","orcid":"https://orcid.org/0009-0007-9938-1331"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher R Cabanski","raw_affiliation_strings":["Department of Statistics and Operations Research, Chapel Hill, NC, USA","Department of Statistics and Operations Research, Chapel Hill, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics and Operations Research, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Statistics and Operations Research, Chapel Hill, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074175904","display_name":"Keary Cavin","orcid":null},"institutions":[{"id":"https://openalex.org/I69048370","display_name":"Renaissance Computing Institute","ror":"https://ror.org/01s91ey96","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535","https://openalex.org/I170897317","https://openalex.org/I69048370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Keary Cavin","raw_affiliation_strings":["Renaissance Computing Center, Chapel Hill, NC, USA","Renaissance Computing Center, Chapel Hill, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Renaissance Computing Center, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I69048370"]},{"raw_affiliation_string":"Renaissance Computing Center, Chapel Hill, USA","institution_ids":["https://openalex.org/I69048370"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043972221","display_name":"Chris Bizon","orcid":null},"institutions":[{"id":"https://openalex.org/I69048370","display_name":"Renaissance Computing Institute","ror":"https://ror.org/01s91ey96","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535","https://openalex.org/I170897317","https://openalex.org/I69048370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Bizon","raw_affiliation_strings":["Renaissance Computing Center, Chapel Hill, NC, USA","Renaissance Computing Center, Chapel Hill, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Renaissance Computing Center, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I69048370"]},{"raw_affiliation_string":"Renaissance Computing Center, Chapel Hill, USA","institution_ids":["https://openalex.org/I69048370"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047751537","display_name":"Matthew D. Wilkerson","orcid":"https://orcid.org/0000-0003-2727-0230"},"institutions":[{"id":"https://openalex.org/I4390039329","display_name":"UNC Lineberger Comprehensive Cancer Center","ror":"https://ror.org/043ehm030","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew D Wilkerson","raw_affiliation_strings":["Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA","Lineberger Comprehensive Cancer Center, Chapel Hill, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I4390039329"]},{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, Chapel Hill, USA","institution_ids":["https://openalex.org/I4390039329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054811851","display_name":"Joel S. Parker","orcid":"https://orcid.org/0000-0003-2080-6901"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I4390039329","display_name":"UNC Lineberger Comprehensive Cancer Center","ror":"https://ror.org/043ehm030","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joel S Parker","raw_affiliation_strings":["Department of Genetics, Chapel Hill, NC, USA","Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA","Department of Genetics, Chapel Hill, USA","Lineberger Comprehensive Cancer Center, Chapel Hill, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I4390039329"]},{"raw_affiliation_string":"Department of Genetics, Chapel Hill, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, Chapel Hill, USA","institution_ids":["https://openalex.org/I4390039329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004390437","display_name":"Kirk C. Wilhelmsen","orcid":"https://orcid.org/0000-0002-4432-8302"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I4390039329","display_name":"UNC Lineberger Comprehensive Cancer Center","ror":"https://ror.org/043ehm030","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]},{"id":"https://openalex.org/I69048370","display_name":"Renaissance Computing Institute","ror":"https://ror.org/01s91ey96","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535","https://openalex.org/I170897317","https://openalex.org/I69048370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kirk C Wilhelmsen","raw_affiliation_strings":["Department of Genetics, Chapel Hill, NC, USA","Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA","Renaissance Computing Center, Chapel Hill, NC, USA","Department of Genetics, Chapel Hill, USA","Lineberger Comprehensive Cancer Center, Chapel Hill, USA","Renaissance Computing Center, Chapel Hill, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I4390039329"]},{"raw_affiliation_string":"Renaissance Computing Center, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I69048370"]},{"raw_affiliation_string":"Department of Genetics, Chapel Hill, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, Chapel Hill, USA","institution_ids":["https://openalex.org/I4390039329"]},{"raw_affiliation_string":"Renaissance Computing Center, Chapel Hill, USA","institution_ids":["https://openalex.org/I69048370"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062498736","display_name":"Charles M. Perou","orcid":"https://orcid.org/0000-0001-9827-2247"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I4390039329","display_name":"UNC Lineberger Comprehensive Cancer Center","ror":"https://ror.org/043ehm030","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charles M Perou","raw_affiliation_strings":["Department of Genetics, Chapel Hill, NC, USA","Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA","Department of Genetics, Chapel Hill, USA","Lineberger Comprehensive Cancer Center, Chapel Hill, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I4390039329"]},{"raw_affiliation_string":"Department of Genetics, Chapel Hill, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, Chapel Hill, USA","institution_ids":["https://openalex.org/I4390039329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060651495","display_name":"J. S. Marron","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I4390039329","display_name":"UNC Lineberger Comprehensive Cancer Center","ror":"https://ror.org/043ehm030","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"JS Marron","raw_affiliation_strings":["Department of Statistics and Operations Research, Chapel Hill, NC, USA","Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA","Department of Statistics and Operations Research, Chapel Hill, USA","Lineberger Comprehensive Cancer Center, Chapel Hill, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics and Operations Research, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I4390039329"]},{"raw_affiliation_string":"Department of Statistics and Operations Research, Chapel Hill, USA","institution_ids":[]},{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, Chapel Hill, USA","institution_ids":["https://openalex.org/I4390039329"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068906036","display_name":"D. Neil Hayes","orcid":"https://orcid.org/0000-0001-6203-7771"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I4390039329","display_name":"UNC Lineberger Comprehensive Cancer Center","ror":"https://ror.org/043ehm030","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"D Neil Hayes","raw_affiliation_strings":["Department of Internal Medicine, Division of Medical Oncology, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA","Department of Internal Medicine, Division of Medical Oncology, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, USA","Lineberger Comprehensive Cancer Center, Chapel Hill, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, Division of Medical Oncology, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I4390039329"]},{"raw_affiliation_string":"Department of Internal Medicine, Division of Medical Oncology, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, Chapel Hill, USA","institution_ids":["https://openalex.org/I4390039329"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5068906036"],"corresponding_institution_ids":["https://openalex.org/I114027177","https://openalex.org/I4390039329"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.491,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.63139268,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"13","issue":"1","first_page":"221","last_page":"221"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8137999773025513,"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":0.8137999773025513,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.05079999938607216,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.038100000470876694,"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/bioconductor","display_name":"Bioconductor","score":0.9363319277763367},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.637397825717926},{"id":"https://openalex.org/keywords/quality-score","display_name":"Quality Score","score":0.6048678755760193},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.5801708698272705},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5339635014533997},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5184511542320251},{"id":"https://openalex.org/keywords/logistic-regression","display_name":"Logistic regression","score":0.5055627822875977},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.500962495803833},{"id":"https://openalex.org/keywords/data-quality","display_name":"Data quality","score":0.4161022901535034},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3702961206436157},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.23680898547172546},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1754986047744751},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.16944748163223267},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1683897078037262},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11143076419830322},{"id":"https://openalex.org/keywords/operations-management","display_name":"Operations management","score":0.10016223788261414},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07968246936798096}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9363319277763367},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.637397825717926},{"id":"https://openalex.org/C2779346075","wikidata":"https://www.wikidata.org/wiki/Q7268763","display_name":"Quality Score","level":3,"score":0.6048678755760193},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.5801708698272705},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5339635014533997},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5184511542320251},{"id":"https://openalex.org/C151956035","wikidata":"https://www.wikidata.org/wiki/Q1132755","display_name":"Logistic regression","level":2,"score":0.5055627822875977},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.500962495803833},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.4161022901535034},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3702961206436157},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.23680898547172546},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1754986047744751},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.16944748163223267},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1683897078037262},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11143076419830322},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.10016223788261414},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07968246936798096},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D016015","descriptor_name":"Logistic Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016015","descriptor_name":"Logistic Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016015","descriptor_name":"Logistic Models","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":"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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-13-221","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-221","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-221","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:22946927","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22946927","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:europepmc.org:2450021","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3447716","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:cdr.lib.unc.edu:uuid:b178e043-cd14-4223-8780-dd7d4c1e39e2","is_oa":true,"landing_page_url":"https://cdr.lib.unc.edu/record/uuid:b178e043-cd14-4223-8780-dd7d4c1e39e2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401075","display_name":"Carolina Digital Repository (University of North Carolina at Chapel Hill)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I114027177","host_organization_name":"University of North Carolina at Chapel Hill","host_organization_lineage":["https://openalex.org/I114027177"],"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":"","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:1b19918c8e124e9cb9ef86f0b300690e","is_oa":false,"landing_page_url":"https://doaj.org/article/1b19918c8e124e9cb9ef86f0b300690e","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 13, Iss 1, p 221 (2012)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-221","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-221","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-221","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":[{"id":"https://metadata.un.org/sdg/10","score":0.6399999856948853,"display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G1569999668","display_name":null,"funder_award_id":"P50 CA058223","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G232243944","display_name":null,"funder_award_id":"P30 CA016086","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2794530620","display_name":"Gene Expression Patterns in Human Tumors Identified Using Transcript Sequencing","funder_award_id":"3u24ca143848-05s2","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2894286751","display_name":null,"funder_award_id":"U24-CA143848","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3394353484","display_name":null,"funder_award_id":"F32 CA142039","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3829197932","display_name":null,"funder_award_id":"DA030976","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"},{"id":"https://openalex.org/G44794847","display_name":"Deep sequencing studies for cannabis and stimulant dependence","funder_award_id":"5r01da030976-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6130065715","display_name":null,"funder_award_id":"U24 CA143848-02S1","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6539020369","display_name":null,"funder_award_id":"1R01-DA030976-01","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337347","display_name":"National Institute on Drug Abuse","ror":"https://ror.org/00fq5cm18"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2105868188.pdf","grobid_xml":"https://content.openalex.org/works/W2105868188.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1926851645","https://openalex.org/W2021341670","https://openalex.org/W2082376103","https://openalex.org/W2083854815","https://openalex.org/W2108234281","https://openalex.org/W2119923823","https://openalex.org/W2121016876","https://openalex.org/W2124960286","https://openalex.org/W2126144698","https://openalex.org/W2127515057","https://openalex.org/W2131016694","https://openalex.org/W2131088968","https://openalex.org/W2143173327","https://openalex.org/W2160697532","https://openalex.org/W2168133698","https://openalex.org/W2324171367"],"related_works":["https://openalex.org/W2982252354","https://openalex.org/W2728564446","https://openalex.org/W3045904767","https://openalex.org/W2161868542","https://openalex.org/W2140163842","https://openalex.org/W3156537409","https://openalex.org/W2747931568","https://openalex.org/W2133055377","https://openalex.org/W2921090651","https://openalex.org/W2287365612"],"abstract_inverted_index":{"BACKGROUND:":[0],"Next-generation":[1],"sequencing":[2,66,107,117,173],"technologies":[3],"have":[4,21,39],"become":[5],"important":[6],"tools":[7,134],"for":[8,166,171],"genome-wide":[9],"studies.":[10],"However,":[11],"the":[12,28,44,55,77,80,95,103,122,189,200,203],"quality":[13,29,57,87,124,148,169,184],"scores":[14,30,58,88,170],"that":[15,53,84,89,97,137],"are":[16,31,90],"assigned":[17],"to":[18,24,102,130],"each":[19],"base":[20,56,168],"been":[22],"shown":[23],"be":[25],"inaccurate.":[26],"If":[27],"used":[32],"in":[33,94,145,160],"downstream":[34,192],"analyses,":[35],"these":[36],"inaccuracies":[37],"can":[38,187],"a":[40,51,106,111,177],"significant":[41],"impact":[42],"on":[43],"results.":[45],"RESULTS:":[46],"Here":[47],"we":[48],"present":[49],"ReQON,":[50],"tool":[52],"recalibrates":[54],"from":[59],"an":[60,154],"input":[61],"BAM":[62,179],"file":[63,180],"of":[64,79,105,114,147,191,202],"aligned":[65],"data":[67],"using":[68],"logistic":[69],"regression.":[70],"ReQON":[71,85,129,138,152,175],"also":[72,127],"generates":[73],"diagnostic":[74,197],"plots":[75,198],"showing":[76,199],"effectiveness":[78,201],"recalibration.":[81,204],"We":[82,126],"show":[83,136],"produces":[86,176,195],"both":[91],"more":[92,99,182],"accurate,":[93],"sense":[96],"they":[98],"closely":[100],"correspond":[101],"probability":[104],"error,":[108],"and":[109,119,135,142,162,194],"do":[110],"better":[112],"job":[113],"discriminating":[115],"between":[116],"errors":[118],"non-errors":[120],"than":[121],"original":[123],"scores.":[125],"compare":[128],"other":[131],"available":[132,163],"recalibration":[133],"is":[139,153],"less":[140],"biased":[141],"performs":[143],"favorably":[144],"terms":[146],"score":[149],"accuracy.":[150],"CONCLUSION:":[151],"open":[155],"source":[156],"software":[157],"package,":[158],"written":[159],"R":[161],"through":[164],"Bioconductor,":[165],"recalibrating":[167],"next-generation":[172],"data.":[174],"new":[178],"with":[181],"accurate":[183],"scores,":[185],"which":[186],"improve":[188],"results":[190],"analysis,":[193],"several":[196]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
