{"id":"https://openalex.org/W3003747570","doi":"https://doi.org/10.1093/bioinformatics/btaa053","title":"UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries","display_name":"UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries","publication_year":2020,"publication_date":"2020-01-20","ids":{"openalex":"https://openalex.org/W3003747570","doi":"https://doi.org/10.1093/bioinformatics/btaa053","mag":"3003747570","pmid":"https://pubmed.ncbi.nlm.nih.gov/31985795"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa053","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa053","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2718/33180859/btaa053.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/36/9/2718/33180859/btaa053.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090193963","display_name":"Vincent Sater","orcid":"https://orcid.org/0000-0003-1976-5954"},"institutions":[{"id":"https://openalex.org/I4210105918","display_name":"Normandie Universit\u00e9","ror":"https://ror.org/01k40cz91","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918"]},{"id":"https://openalex.org/I4210108118","display_name":"Laboratoire d'Informatique, du Traitement de l'Information et des Syst\u00e8mes","ror":"https://ror.org/01f1vfy95","country_code":"FR","type":"facility","lineage":["https://openalex.org/I141576021","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210108118","https://openalex.org/I62396329","https://openalex.org/I88814501"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Vincent Sater","raw_affiliation_strings":["University of Normandie UNIROUEN , LITIS EA 4108"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Normandie UNIROUEN , LITIS EA 4108","institution_ids":["https://openalex.org/I4210105918","https://openalex.org/I4210108118"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049252531","display_name":"Pierre\u2010Julien Viailly","orcid":"https://orcid.org/0000-0002-9636-8971"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210105918","display_name":"Normandie Universit\u00e9","ror":"https://ror.org/01k40cz91","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918"]},{"id":"https://openalex.org/I4387152093","display_name":"Centre Henri Becquerel","ror":"https://ror.org/00whhby07","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210141925","https://openalex.org/I4387152093"]},{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pierre-Julien Viailly","raw_affiliation_strings":["Department of Pathology , Centre Henri Becquerel","INSERM U1245 , University of Normandie UNIROUEN, Rouen 76000, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology , Centre Henri Becquerel","institution_ids":["https://openalex.org/I4387152093"]},{"raw_affiliation_string":"INSERM U1245 , University of Normandie UNIROUEN, Rouen 76000, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I4210105918","https://openalex.org/I62396329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052475314","display_name":"Thierry Lecroq","orcid":"https://orcid.org/0000-0002-1900-3397"},"institutions":[{"id":"https://openalex.org/I4210105918","display_name":"Normandie Universit\u00e9","ror":"https://ror.org/01k40cz91","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918"]},{"id":"https://openalex.org/I4210108118","display_name":"Laboratoire d'Informatique, du Traitement de l'Information et des Syst\u00e8mes","ror":"https://ror.org/01f1vfy95","country_code":"FR","type":"facility","lineage":["https://openalex.org/I141576021","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210108118","https://openalex.org/I62396329","https://openalex.org/I88814501"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Thierry Lecroq","raw_affiliation_strings":["University of Normandie UNIROUEN , LITIS EA 4108"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Normandie UNIROUEN , LITIS EA 4108","institution_ids":["https://openalex.org/I4210105918","https://openalex.org/I4210108118"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110513210","display_name":"\u00c9lise Prieur-Gaston","orcid":null},"institutions":[{"id":"https://openalex.org/I4210105918","display_name":"Normandie Universit\u00e9","ror":"https://ror.org/01k40cz91","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918"]},{"id":"https://openalex.org/I4210108118","display_name":"Laboratoire d'Informatique, du Traitement de l'Information et des Syst\u00e8mes","ror":"https://ror.org/01f1vfy95","country_code":"FR","type":"facility","lineage":["https://openalex.org/I141576021","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210108118","https://openalex.org/I62396329","https://openalex.org/I88814501"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"\u00c9lise Prieur-Gaston","raw_affiliation_strings":["University of Normandie UNIROUEN , LITIS EA 4108"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Normandie UNIROUEN , LITIS EA 4108","institution_ids":["https://openalex.org/I4210105918","https://openalex.org/I4210108118"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039451592","display_name":"\u00c9lodie Bohers","orcid":"https://orcid.org/0000-0001-9168-576X"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210105918","display_name":"Normandie Universit\u00e9","ror":"https://ror.org/01k40cz91","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918"]},{"id":"https://openalex.org/I4387152093","display_name":"Centre Henri Becquerel","ror":"https://ror.org/00whhby07","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210141925","https://openalex.org/I4387152093"]},{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"\u00c9lodie Bohers","raw_affiliation_strings":["Department of Pathology , Centre Henri Becquerel","INSERM U1245 , University of Normandie UNIROUEN, Rouen 76000, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology , Centre Henri Becquerel","institution_ids":["https://openalex.org/I4387152093"]},{"raw_affiliation_string":"INSERM U1245 , University of Normandie UNIROUEN, Rouen 76000, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I4210105918","https://openalex.org/I62396329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046312843","display_name":"Mathieu Viennot","orcid":null},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210105918","display_name":"Normandie Universit\u00e9","ror":"https://ror.org/01k40cz91","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918"]},{"id":"https://openalex.org/I4387152093","display_name":"Centre Henri Becquerel","ror":"https://ror.org/00whhby07","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210141925","https://openalex.org/I4387152093"]},{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Mathieu Viennot","raw_affiliation_strings":["Department of Pathology , Centre Henri Becquerel","INSERM U1245 , University of Normandie UNIROUEN, Rouen 76000, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology , Centre Henri Becquerel","institution_ids":["https://openalex.org/I4387152093"]},{"raw_affiliation_string":"INSERM U1245 , University of Normandie UNIROUEN, Rouen 76000, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I4210105918","https://openalex.org/I62396329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113544453","display_name":"Philippe Ruminy","orcid":"https://orcid.org/0000-0003-1548-4848"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210105918","display_name":"Normandie Universit\u00e9","ror":"https://ror.org/01k40cz91","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918"]},{"id":"https://openalex.org/I4387152093","display_name":"Centre Henri Becquerel","ror":"https://ror.org/00whhby07","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210141925","https://openalex.org/I4387152093"]},{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Philippe Ruminy","raw_affiliation_strings":["Department of Pathology , Centre Henri Becquerel","INSERM U1245 , University of Normandie UNIROUEN, Rouen 76000, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology , Centre Henri Becquerel","institution_ids":["https://openalex.org/I4387152093"]},{"raw_affiliation_string":"INSERM U1245 , University of Normandie UNIROUEN, Rouen 76000, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I4210105918","https://openalex.org/I62396329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065843661","display_name":"H\u00e9l\u00e8ne Dauchel","orcid":"https://orcid.org/0000-0003-3156-9737"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210105918","display_name":"Normandie Universit\u00e9","ror":"https://ror.org/01k40cz91","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918"]},{"id":"https://openalex.org/I4387152093","display_name":"Centre Henri Becquerel","ror":"https://ror.org/00whhby07","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210141925","https://openalex.org/I4387152093"]},{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"H\u00e9l\u00e8ne Dauchel","raw_affiliation_strings":["Department of Pathology , Centre Henri Becquerel","INSERM U1245 , University of Normandie UNIROUEN, Rouen 76000, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology , Centre Henri Becquerel","institution_ids":["https://openalex.org/I4387152093"]},{"raw_affiliation_string":"INSERM U1245 , University of Normandie UNIROUEN, Rouen 76000, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I4210105918","https://openalex.org/I62396329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111409512","display_name":"Pierre V\u00e9ra","orcid":null},"institutions":[{"id":"https://openalex.org/I4210105918","display_name":"Normandie Universit\u00e9","ror":"https://ror.org/01k40cz91","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918"]},{"id":"https://openalex.org/I4210108118","display_name":"Laboratoire d'Informatique, du Traitement de l'Information et des Syst\u00e8mes","ror":"https://ror.org/01f1vfy95","country_code":"FR","type":"facility","lineage":["https://openalex.org/I141576021","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210108118","https://openalex.org/I62396329","https://openalex.org/I88814501"]},{"id":"https://openalex.org/I4387152093","display_name":"Centre Henri Becquerel","ror":"https://ror.org/00whhby07","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210141925","https://openalex.org/I4387152093"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pierre Vera","raw_affiliation_strings":["Department of Pathology , Centre Henri Becquerel","University of Normandie UNIROUEN , LITIS EA 4108","Equipe Quantification en Imagerie Fonctionnelle"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology , Centre Henri Becquerel","institution_ids":["https://openalex.org/I4387152093"]},{"raw_affiliation_string":"University of Normandie UNIROUEN , LITIS EA 4108","institution_ids":["https://openalex.org/I4210105918","https://openalex.org/I4210108118"]},{"raw_affiliation_string":"Equipe Quantification en Imagerie Fonctionnelle","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082700087","display_name":"Fabrice Jardin","orcid":"https://orcid.org/0000-0002-6804-7943"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210105918","display_name":"Normandie Universit\u00e9","ror":"https://ror.org/01k40cz91","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918"]},{"id":"https://openalex.org/I4387152093","display_name":"Centre Henri Becquerel","ror":"https://ror.org/00whhby07","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210141925","https://openalex.org/I4387152093"]},{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fabrice Jardin","raw_affiliation_strings":["Department of Pathology , Centre Henri Becquerel","INSERM U1245 , University of Normandie UNIROUEN, Rouen 76000, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology , Centre Henri Becquerel","institution_ids":["https://openalex.org/I4387152093"]},{"raw_affiliation_string":"INSERM U1245 , University of Normandie UNIROUEN, Rouen 76000, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I4210105918","https://openalex.org/I62396329"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5090193963"],"corresponding_institution_ids":["https://openalex.org/I4210105918","https://openalex.org/I4210108118"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2015,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":{"value":0.76106282,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"36","issue":"9","first_page":"2718","last_page":"2724"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.859000027179718,"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"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.859000027179718,"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"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.030899999663233757,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.027699999511241913,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5277760028839111},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4507470428943634},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2712247669696808}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5277760028839111},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4507470428943634},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2712247669696808}],"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":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","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":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","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":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa053","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa053","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2718/33180859/btaa053.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:31985795","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31985795","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},{"id":"pmh:oai:HAL:hal-02468271v1","is_oa":false,"landing_page_url":"https://hal.science/hal-02468271","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2020, 36 (9), pp.2718-2724. &#x27E8;10.1093/bioinformatics/btaa053&#x27E9;","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa053","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa053","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2718/33180859/btaa053.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":[{"display_name":"Industry, innovation and infrastructure","score":0.5099999904632568,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320329938","display_name":"R\u00e9gion Normandie","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W2053218599","https://openalex.org/W2064296460","https://openalex.org/W2108234281","https://openalex.org/W2110065044","https://openalex.org/W2143197030","https://openalex.org/W2151794156","https://openalex.org/W2303585199","https://openalex.org/W2329906190","https://openalex.org/W2394588964","https://openalex.org/W2511116391","https://openalex.org/W2517179206","https://openalex.org/W2547285282","https://openalex.org/W2560033121","https://openalex.org/W2611802561","https://openalex.org/W2807488560","https://openalex.org/W2952901975"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"MOTIVATION:":[0],"Next-generation":[1],"sequencing":[2,30,71,125,244],"has":[3,73],"become":[4],"the":[5,10,89,95,145,151,179,183,186,200,203,209,237,243],"go-to":[6],"standard":[7],"method":[8],"for":[9,123],"detection":[11],"of":[12,20,64,91,150,202,216,245],"single-nucleotide":[13],"variants":[14,50,82],"in":[15,33,55,69,94,139,182],"tumor":[16,56,246],"cells.":[17],"The":[18,61,267],"use":[19,63],"such":[21],"technologies":[22],"requires":[23],"a":[24,29,75,119,188,221,225],"PCR":[25],"amplification":[26],"step":[27],"and":[28,58,83,107,224,248,256],"step,":[31],"steps":[32],"which":[34],"artifacts":[35,43],"are":[36,44,104,229,281],"introduced":[37],"at":[38,166,194,272,283],"very":[39],"low":[40],"frequencies.":[41],"These":[42],"often":[45],"confused":[46],"with":[47,127,137],"true":[48],"low-frequency":[49,86],"that":[51,103,155],"can":[52],"be":[53],"found":[54],"cells":[57],"cell-free":[59],"DNA.":[60],"recent":[62],"unique":[65],"molecular":[66],"identifiers":[67],"(UMI)":[68],"targeted":[70,124],"protocols":[72],"offered":[74],"trustworthy":[76],"approach":[77],"to":[78,100,131,161,177,197,231],"filter":[79,228],"out":[80,143],"artefactual":[81],"accurately":[84],"call":[85],"variants.":[87],"However,":[88],"integration":[90],"UMI":[92,180,217],"analysis":[93,215],"variant":[96,113,121,133,153,204],"calling":[97],"process":[98],"led":[99],"developing":[101],"tools":[102],"significantly":[105,206],"slower":[106],"more":[108,257],"memory":[109],"consuming":[110],"than":[111,208,259],"raw-reads-based":[112],"callers.":[114,134],"RESULTS:":[115],"We":[116,235],"present":[117],"UMI-VarCal,":[118],"UMI-based":[120],"caller":[122],"data":[126,280],"better":[128,233],"sensitivity":[129],"compared":[130],"other":[132,260],"Being":[135],"developed":[136],"performance":[138],"mind,":[140],"UMI-VarCal":[141,241,252],"stands":[142],"from":[144],"crowd":[146],"by":[147],"being":[148],"one":[149],"few":[152],"callers":[154],"do":[156,162],"not":[157],"rely":[158],"on":[159],"SAMtools":[160],"their":[163],"pileup.":[164],"Instead,":[165],"its":[167],"core":[168],"runs":[169],"an":[170,214],"innovative":[171],"homemade":[172],"pileup":[173],"algorithm":[174],"specifically":[175],"designed":[176],"treat":[178],"tags":[181,218],"reads.":[184],"After":[185],"pileup,":[187],"Poisson":[189],"statistical":[190],"test":[191],"is":[192,205,219,253,270],"applied":[193,230],"every":[195],"position":[196],"determine":[198],"if":[199],"frequency":[201],"higher":[207],"background":[210],"error":[211],"noise.":[212],"Finally,":[213],"performed,":[220],"strand":[222],"bias":[223],"homopolymer":[226],"length":[227],"achieve":[232],"accuracy.":[234],"illustrate":[236],"results":[238],"obtained":[239],"using":[240],"through":[242],"samples":[247],"we":[249],"show":[250],"how":[251],"both":[254],"faster":[255],"sensitive":[258],"publicly":[261],"available":[262,271,282],"solutions.":[263],"AVAILABILITY":[264],"AND":[265],"IMPLEMENTATION:":[266],"entire":[268],"pipeline":[269],"https://gitlab.com/vincent-sater/umi-varcal-master":[273],"under":[274],"MIT":[275],"license.":[276],"SUPPLEMENTARY":[277],"INFORMATION:":[278],"Supplementary":[279],"Bioinformatics":[284],"online.":[285]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
