{"id":"https://openalex.org/W4386624113","doi":"https://doi.org/10.3233/shti230694","title":"Onkopipe: A Snakemake Based DNA-Sequencing Pipeline for Clinical Variant Analysis in Precision Medicine","display_name":"Onkopipe: A Snakemake Based DNA-Sequencing Pipeline for Clinical Variant Analysis in Precision Medicine","publication_year":2023,"publication_date":"2023-09-12","ids":{"openalex":"https://openalex.org/W4386624113","doi":"https://doi.org/10.3233/shti230694","pmid":"https://pubmed.ncbi.nlm.nih.gov/37697838"},"language":"en","primary_location":{"id":"doi:10.3233/shti230694","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3233/shti230694","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI230694","source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI230694","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063288559","display_name":"Jingyu Yang","orcid":"https://orcid.org/0000-0002-7521-7920"},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jingyu Yang","raw_affiliation_strings":["Department of Medical Bioinformatics, University of G\u00f6ttingen, G\u00f6ttingen, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Medical Bioinformatics, University of G\u00f6ttingen, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017944645","display_name":"Tim Bei\u00dfbarth","orcid":"https://orcid.org/0000-0001-6509-2143"},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]},{"id":"https://openalex.org/I4210152261","display_name":"Intelligent Transport Systems Niedersachsen","ror":"https://ror.org/05xyrf554","country_code":"DE","type":"other","lineage":["https://openalex.org/I4210152261"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tim Bei\u00dfbarth","raw_affiliation_strings":["Campus-Institute Data Science (CIDAS), University of G\u00f6ttingen, G\u00f6ttingen, Germany","Comprehensive Cancer Center Niedersachsen (CCCN), G\u00f6ttingen, Germany","Department of Medical Bioinformatics, University of G\u00f6ttingen, G\u00f6ttingen, Germany"],"affiliations":[{"raw_affiliation_string":"Campus-Institute Data Science (CIDAS), University of G\u00f6ttingen, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]},{"raw_affiliation_string":"Comprehensive Cancer Center Niedersachsen (CCCN), G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I4210152261"]},{"raw_affiliation_string":"Department of Medical Bioinformatics, University of G\u00f6ttingen, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010196918","display_name":"J\u00fcrgen D\u00f6nitz","orcid":"https://orcid.org/0000-0002-8401-8851"},"institutions":[{"id":"https://openalex.org/I4210152261","display_name":"Intelligent Transport Systems Niedersachsen","ror":"https://ror.org/05xyrf554","country_code":"DE","type":"other","lineage":["https://openalex.org/I4210152261"]},{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"J\u00fcrgen D\u00f6nitz","raw_affiliation_strings":["Campus-Institute Data Science (CIDAS), University of G\u00f6ttingen, G\u00f6ttingen, Germany","Comprehensive Cancer Center Niedersachsen (CCCN), G\u00f6ttingen, Germany","Department of Medical Bioinformatics, University of G\u00f6ttingen, G\u00f6ttingen, Germany"],"affiliations":[{"raw_affiliation_string":"Campus-Institute Data Science (CIDAS), University of G\u00f6ttingen, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]},{"raw_affiliation_string":"Comprehensive Cancer Center Niedersachsen (CCCN), G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I4210152261"]},{"raw_affiliation_string":"Department of Medical Bioinformatics, University of G\u00f6ttingen, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5010196918"],"corresponding_institution_ids":["https://openalex.org/I4210152261","https://openalex.org/I74656192"],"apc_list":null,"apc_paid":null,"fwci":1.5654,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.8429003,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"307","issue":null,"first_page":"60","last_page":"68"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9958000183105469,"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":0.9937000274658203,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7484368681907654},{"id":"https://openalex.org/keywords/precision-medicine","display_name":"Precision medicine","score":0.6854074597358704},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6839994192123413},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.5983912348747253},{"id":"https://openalex.org/keywords/concordance","display_name":"Concordance","score":0.4840032756328583},{"id":"https://openalex.org/keywords/personalized-medicine","display_name":"Personalized medicine","score":0.45021185278892517},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.4207204580307007},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4131469130516052},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3411622643470764},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.20475468039512634},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.18753516674041748},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17145183682441711},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13741564750671387},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.11330381035804749},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09076648950576782},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0665108859539032}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7484368681907654},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.6854074597358704},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6839994192123413},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5983912348747253},{"id":"https://openalex.org/C160798450","wikidata":"https://www.wikidata.org/wiki/Q4230870","display_name":"Concordance","level":2,"score":0.4840032756328583},{"id":"https://openalex.org/C32220436","wikidata":"https://www.wikidata.org/wiki/Q2072214","display_name":"Personalized medicine","level":2,"score":0.45021185278892517},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.4207204580307007},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4131469130516052},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3411622643470764},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.20475468039512634},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.18753516674041748},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17145183682441711},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13741564750671387},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.11330381035804749},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09076648950576782},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0665108859539032}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","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":"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":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.3233/shti230694","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3233/shti230694","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI230694","source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},{"id":"pmid:37697838","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37697838","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":"Studies in health technology and informatics","raw_type":null},{"id":"pmh:oai:publications.goettingen-research-online.de:2/133099","is_oa":true,"landing_page_url":"https://resolver.sub.uni-goettingen.de/purl?gro-2/133099","pdf_url":null,"source":{"id":"https://openalex.org/S4306401634","display_name":"GoeScholar  The Publication Server of the Georg-August-Universit\u00e4t G\u00f6ttingen (Georg-August-Universit\u00e4t G\u00f6ttingen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210122495","host_organization_name":"Asklepios Klinik St. Georg","host_organization_lineage":["https://openalex.org/I4210122495"],"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":"yes"}],"best_oa_location":{"id":"doi:10.3233/shti230694","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3233/shti230694","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI230694","source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386624113.pdf","grobid_xml":"https://content.openalex.org/works/W4386624113.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1919257374","https://openalex.org/W2000528034","https://openalex.org/W2103441770","https://openalex.org/W2108234281","https://openalex.org/W2110417468","https://openalex.org/W2111350087","https://openalex.org/W2124796057","https://openalex.org/W2136939537","https://openalex.org/W2138601221","https://openalex.org/W2150131459","https://openalex.org/W2337209831","https://openalex.org/W2558624268","https://openalex.org/W2748728020","https://openalex.org/W2802080790","https://openalex.org/W2803247374","https://openalex.org/W2929354011","https://openalex.org/W2959872456","https://openalex.org/W3006716981","https://openalex.org/W3012203069","https://openalex.org/W3016255499","https://openalex.org/W3033196316","https://openalex.org/W3044880600","https://openalex.org/W3094099042","https://openalex.org/W3125012412","https://openalex.org/W3125032632","https://openalex.org/W3151257524","https://openalex.org/W3158170126","https://openalex.org/W4229072282","https://openalex.org/W4283210431","https://openalex.org/W4283574508","https://openalex.org/W4292133664","https://openalex.org/W6950152225"],"related_works":["https://openalex.org/W3082935376","https://openalex.org/W3193951088","https://openalex.org/W4322484660","https://openalex.org/W2899657781","https://openalex.org/W4386960999","https://openalex.org/W2770866531","https://openalex.org/W4388011470","https://openalex.org/W4230423494","https://openalex.org/W4298001029","https://openalex.org/W3176719936"],"abstract_inverted_index":{"NGS":[0],"is":[1,40,79,120,129],"increasingly":[2],"used":[3],"in":[4,69,97],"precision":[5,98],"medicine,":[6],"but":[7],"an":[8,124],"automated":[9],"sequencing":[10],"pipeline":[11,50],"that":[12,51],"can":[13],"detect":[14,64],"different":[15],"types":[16],"of":[17,94],"variants":[18],"(single":[19],"nucleotide":[20],"-":[21,25,28],"SNV,":[22,65],"copy":[23],"number":[24],"CNV,":[26,66],"structural":[27],"SV)":[29],"and":[30,59,67,81,88,102,107,128],"does":[31],"not":[32],"rely":[33],"on":[34],"normal":[35,76],"samples":[36],"as":[37,85,123],"germline":[38],"comparison":[39],"needed.":[41],"To":[42],"address":[43],"this,":[44],"we":[45],"developed":[46],"Onkopipe,":[47],"a":[48,70,111],"Snakemake-based":[49],"integrates":[52],"quality":[53],"control,":[54],"read":[55],"alignments,":[56],"BAM":[57],"pre-processing,":[58],"variant":[60],"calling":[61],"tools":[62],"to":[63],"SV":[68],"unified":[71],"VCF":[72],"format":[73],"without":[74],"matched":[75],"samples.":[77],"Onkopipe":[78,110,119],"containerized":[80],"provides":[82],"features":[83],"such":[84],"reproducibility,":[86],"parallelization,":[87],"easy":[89],"customization,":[90],"enabling":[91],"the":[92],"analysis":[93],"genomic":[95],"data":[96],"medicine.":[99],"Our":[100],"validation":[101],"evaluation":[103],"demonstrate":[104],"high":[105],"accuracy":[106],"concordance,":[108],"making":[109],"valuable":[112],"open-source":[113],"resource":[114],"for":[115],"molecular":[116],"tumor":[117],"boards.":[118],"being":[121],"shared":[122],"open":[125],"source":[126],"project":[127],"available":[130],"at":[131],"https://gitlab.gwdg.de/MedBioinf/mtb/onkopipe.":[132]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2025-12-25T23:11:45.687758","created_date":"2025-10-10T00:00:00"}
