{"id":"https://openalex.org/W4406932472","doi":"https://doi.org/10.1093/bib/bbaf035","title":"SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline","display_name":"SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4406932472","doi":"https://doi.org/10.1093/bib/bbaf035","pmid":"https://pubmed.ncbi.nlm.nih.gov/39879385"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf035","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbaf035/61666590/bbaf035.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/1/bbaf035/61666590/bbaf035.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107673623","display_name":"Sara Potente","orcid":null},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Sara Potente","raw_affiliation_strings":["Department of Biology, University of Padova , Via U.Bassi 58/ B, 35131 ,"],"raw_orcid":"https://orcid.org/0009-0007-5514-9389","affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova , Via U.Bassi 58/ B, 35131 ,","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079874954","display_name":"D. Boscarino","orcid":"https://orcid.org/0009-0003-5774-1723"},"institutions":[{"id":"https://openalex.org/I4210162134","display_name":"Ab Analitica (Italy)","ror":"https://ror.org/05dmnc009","country_code":"IT","type":"company","lineage":["https://openalex.org/I4210162134"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Diego Boscarino","raw_affiliation_strings":["AB Analitica S.r.l. , Via Svizzera, 16, 35127, Padova ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AB Analitica S.r.l. , Via Svizzera, 16, 35127, Padova ,","institution_ids":["https://openalex.org/I4210162134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064250806","display_name":"Dino Paladin","orcid":"https://orcid.org/0009-0004-2996-1195"},"institutions":[{"id":"https://openalex.org/I4210162134","display_name":"Ab Analitica (Italy)","ror":"https://ror.org/05dmnc009","country_code":"IT","type":"company","lineage":["https://openalex.org/I4210162134"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Dino Paladin","raw_affiliation_strings":["AB Analitica S.r.l. , Via Svizzera, 16, 35127, Padova ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AB Analitica S.r.l. , Via Svizzera, 16, 35127, Padova ,","institution_ids":["https://openalex.org/I4210162134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069986334","display_name":"Sergio Marchini","orcid":"https://orcid.org/0000-0003-1783-7651"},"institutions":[{"id":"https://openalex.org/I4210163047","display_name":"IRCCS Humanitas Research Hospital","ror":"https://ror.org/05d538656","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210153126","https://openalex.org/I4210163047"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Sergio Marchini","raw_affiliation_strings":["IRCCS Humanitas Research Hospital , Via Alessandro Manzoni 56, 20089 Rozzano, Milano ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IRCCS Humanitas Research Hospital , Via Alessandro Manzoni 56, 20089 Rozzano, Milano ,","institution_ids":["https://openalex.org/I4210163047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039120460","display_name":"Luca Beltrame","orcid":"https://orcid.org/0000-0003-3631-6544"},"institutions":[{"id":"https://openalex.org/I4210163047","display_name":"IRCCS Humanitas Research Hospital","ror":"https://ror.org/05d538656","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210153126","https://openalex.org/I4210163047"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Luca Beltrame","raw_affiliation_strings":["IRCCS Humanitas Research Hospital , Via Alessandro Manzoni 56, 20089 Rozzano, Milano ,"],"raw_orcid":"https://orcid.org/0000-0003-3631-6544","affiliations":[{"raw_affiliation_string":"IRCCS Humanitas Research Hospital , Via Alessandro Manzoni 56, 20089 Rozzano, Milano ,","institution_ids":["https://openalex.org/I4210163047"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082717632","display_name":"Chiara Romualdi","orcid":"https://orcid.org/0000-0003-4792-9047"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Chiara Romualdi","raw_affiliation_strings":["Department of Biology, University of Padova , Via U.Bassi 58/ B, 35131 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova , Via U.Bassi 58/ B, 35131 ,","institution_ids":["https://openalex.org/I138689650"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5039120460"],"corresponding_institution_ids":["https://openalex.org/I4210163047"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.3593,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.59776802,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"26","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9991999864578247,"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":0.9991999864578247,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9976000189781189,"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":0.9959999918937683,"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/pipeline","display_name":"Pipeline (software)","score":0.8105040788650513},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5198062658309937},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5162017941474915},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.39269158244132996},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23155975341796875},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07023084163665771}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8105040788650513},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5198062658309937},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5162017941474915},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.39269158244132996},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23155975341796875},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07023084163665771}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf035","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbaf035/61666590/bbaf035.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39879385","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39879385","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11775468","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11775468","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11775468/pdf/bbaf035.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:www.research.unipd.it:11577/3555826","is_oa":false,"landing_page_url":"https://hdl.handle.net/11577/3555826","pdf_url":null,"source":{"id":"https://openalex.org/S4306402547","display_name":"Padua Research Archive (University of Padova)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf035","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbaf035/61666590/bbaf035.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1223460554","display_name":null,"funder_award_id":"30381","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"},{"id":"https://openalex.org/G2911744495","display_name":null,"funder_award_id":"IG29071","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"},{"id":"https://openalex.org/G434337789","display_name":null,"funder_award_id":"HORIZON2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5356239126","display_name":null,"funder_award_id":"CN00000013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6702624291","display_name":null,"funder_award_id":"IG2024","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"},{"id":"https://openalex.org/G714363581","display_name":null,"funder_award_id":"CN00000013 CN1","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8000286611","display_name":"Improved clinical decisions via integrating multiple data levels to overcome chemotherapy resistance in high-grade serous ovarian cancer","funder_award_id":"965193","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320309832","display_name":"Fondazione Cassa di Risparmio di Padova e Rovigo","ror":"https://ror.org/02jecj653"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406932472.pdf","grobid_xml":"https://content.openalex.org/works/W4406932472.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1848483543","https://openalex.org/W1978645448","https://openalex.org/W2034197594","https://openalex.org/W2102619694","https://openalex.org/W2125636389","https://openalex.org/W2128505445","https://openalex.org/W2157852151","https://openalex.org/W2296335794","https://openalex.org/W2415505014","https://openalex.org/W2432815617","https://openalex.org/W2582743722","https://openalex.org/W2605897695","https://openalex.org/W2613409207","https://openalex.org/W2734691271","https://openalex.org/W2765435739","https://openalex.org/W2781895613","https://openalex.org/W2900295924","https://openalex.org/W2907260934","https://openalex.org/W2920143708","https://openalex.org/W2924313543","https://openalex.org/W2950006249","https://openalex.org/W2950820648","https://openalex.org/W2951912016","https://openalex.org/W2953270703","https://openalex.org/W2966632204","https://openalex.org/W2971559821","https://openalex.org/W3004050413","https://openalex.org/W3006653136","https://openalex.org/W3016792797","https://openalex.org/W3017113819","https://openalex.org/W3111779654","https://openalex.org/W3131055609","https://openalex.org/W3131612759","https://openalex.org/W3160531185","https://openalex.org/W3162783973","https://openalex.org/W3186172985","https://openalex.org/W4210644165","https://openalex.org/W4225140236","https://openalex.org/W4282942593","https://openalex.org/W4282965548","https://openalex.org/W4295242484","https://openalex.org/W4302599161","https://openalex.org/W4316664451","https://openalex.org/W4375863320","https://openalex.org/W4388254930","https://openalex.org/W4388523699","https://openalex.org/W4389383633","https://openalex.org/W4392739992","https://openalex.org/W4394666350","https://openalex.org/W4396556737","https://openalex.org/W4396894261","https://openalex.org/W6697144307","https://openalex.org/W6902592109","https://openalex.org/W6921522649"],"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":{"Shallow":[0],"whole-genome":[1],"sequencing":[2],"(sWGS)":[3],"offers":[4],"a":[5,17,20,38,50,70,160],"cost-effective":[6],"approach":[7],"to":[8,118,169],"detect":[9],"copy":[10,79],"number":[11,80],"alterations":[12],"(CNAs).":[13],"However,":[14],"there":[15],"remains":[16],"gap":[18],"for":[19,25,43,76,90,105,181],"standardized":[21,51],"workflow":[22],"specifically":[23,41],"designed":[24,42],"sWGS":[26,47,174],"analysis.":[27],"To":[28,126],"address":[29],"this":[30,33],"need,":[31],"in":[32,49,166,177,183],"work":[34],"we":[35],"present":[36],"SAMURAI,":[37],"bioinformatics":[39],"pipeline":[40,68,140],"analyzing":[44],"CNAs":[45,172],"from":[46,173],"data":[48,77,120,137,147],"and":[52,65,82,122,135,148,158],"reproducible":[53],"manner.":[54],"SAMURAI":[55,114,130,163],"is":[56],"built":[57],"using":[58,133],"established":[59],"community":[60],"standards,":[61],"ensuring":[62],"portability,":[63],"scalability,":[64],"reproducibility.":[66],"The":[67,109,139],"features":[69],"modular":[71],"design":[72],"with":[73,101,144],"independent":[74],"blocks":[75],"preprocessing,":[78],"analysis,":[81],"customized":[83],"reporting.":[84],"Users":[85],"can":[86],"select":[87],"workflows":[88],"tailored":[89],"either":[91],"solid":[92],"or":[93],"liquid":[94],"biopsy":[95],"analysis":[96],"(e.g.":[97],"circulating":[98],"tumor":[99],"DNA),":[100],"specific":[102],"tools":[103],"integrated":[104],"each":[106],"sample":[107],"type.":[108],"final":[110],"report":[111],"generated":[112],"by":[113],"provides":[115],"detailed":[116],"results":[117],"facilitate":[119],"interpretation":[121],"potential":[123],"downstream":[124],"analyses.":[125],"demonstrate":[127],"its":[128],"robustness,":[129],"was":[131],"validated":[132],"simulated":[134],"real-world":[136],"sets.":[138],"achieved":[141],"high":[142],"concordance":[143],"ground":[145],"truth":[146],"maintained":[149],"consistent":[150],"performance":[151],"across":[152],"various":[153],"scenarios.":[154],"By":[155],"promoting":[156],"standardization":[157],"offering":[159],"versatile":[161],"workflow,":[162],"empowers":[164],"researchers":[165],"diverse":[167],"environments":[168],"reliably":[170],"analyze":[171],"data.":[175],"This,":[176],"turn,":[178],"holds":[179],"promise":[180],"advancements":[182],"precision":[184],"medicine.":[185]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-08-09T07:27:16.801131","created_date":"2025-10-10T00:00:00"}