{"id":"https://openalex.org/W4252335603","doi":"https://doi.org/10.12688/f1000research.16665.1","title":"Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants","display_name":"Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants","publication_year":2020,"publication_date":"2020-01-29","ids":{"openalex":"https://openalex.org/W4252335603","doi":"https://doi.org/10.12688/f1000research.16665.1","pmid":"https://pubmed.ncbi.nlm.nih.gov/32269765"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.16665.1","pdf_url":"https://f1000researchdata.s3.amazonaws.com/manuscripts/18214/674fe691-deba-4c62-8c44-2a9f52b63f35_16665_-_bjorn_nystedt.pdf?doi=10.12688/f1000research.16665.1&numberOfBrowsableCollections=27&numberOfBrowsableInstitutionalCollections=5&numberOfBrowsableGateways=27","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"preprint","type_crossref":"journal-article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://f1000researchdata.s3.amazonaws.com/manuscripts/18214/674fe691-deba-4c62-8c44-2a9f52b63f35_16665_-_bjorn_nystedt.pdf?doi=10.12688/f1000research.16665.1&numberOfBrowsableCollections=27&numberOfBrowsableInstitutionalCollections=5&numberOfBrowsableGateways=27","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038046084","display_name":"M. Garcia","orcid":"https://orcid.org/0000-0003-2827-9261"},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I4210125936","display_name":"BioClinicum (Russia)","ror":"https://ror.org/02bw2gt68","country_code":"RU","type":"company","lineage":["https://openalex.org/I4210125936"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["RU","SE"],"is_corresponding":false,"raw_author_name":"Maxime Garcia","raw_affiliation_strings":["Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164"],"affiliations":[{"raw_affiliation_string":"Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I4210125936","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071796340","display_name":"Szilveszter Juhos","orcid":"https://orcid.org/0000-0001-6280-4643"},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I4210125936","display_name":"BioClinicum (Russia)","ror":"https://ror.org/02bw2gt68","country_code":"RU","type":"company","lineage":["https://openalex.org/I4210125936"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["RU","SE"],"is_corresponding":false,"raw_author_name":"Szilveszter Juhos","raw_affiliation_strings":["Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121","Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37","Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164"],"affiliations":[{"raw_affiliation_string":"Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I4210125936","https://openalex.org/I28166907"]},{"raw_affiliation_string":"Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121","institution_ids":["https://openalex.org/I161593684","https://openalex.org/I2800139495"]},{"raw_affiliation_string":"Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103064557","display_name":"Malin Larsson","orcid":"https://orcid.org/0000-0002-9878-0572"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I102134673","display_name":"Link\u00f6ping University","ror":"https://ror.org/05ynxx418","country_code":"SE","type":"education","lineage":["https://openalex.org/I102134673"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Malin Larsson","raw_affiliation_strings":["Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Link\u00f6ping University, Link\u00f6ping, 58183"],"affiliations":[{"raw_affiliation_string":"Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Link\u00f6ping University, Link\u00f6ping, 58183","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I102134673"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023159887","display_name":"Pall I. Olason","orcid":"https://orcid.org/0000-0002-3350-3443"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Pall I. Olason","raw_affiliation_strings":["Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37"],"affiliations":[{"raw_affiliation_string":"Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088798234","display_name":"Marcel Martin","orcid":"https://orcid.org/0000-0002-0680-200X"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Marcel Martin","raw_affiliation_strings":["Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I161593684"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021321610","display_name":"Jesper Eisfeldt","orcid":"https://orcid.org/0000-0003-3716-4917"},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Jesper Eisfeldt","raw_affiliation_strings":["Clinical Genetics, Department of Molecular Medicine and Surgery, Karolinska Institutet, MMK L1:00, Karolinska University Hospital at Solna, Stockholm, 171 76"],"affiliations":[{"raw_affiliation_string":"Clinical Genetics, Department of Molecular Medicine and Surgery, Karolinska Institutet, MMK L1:00, Karolinska University Hospital at Solna, Stockholm, 171 76","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082330349","display_name":"Sebastian DiLorenzo","orcid":null},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Sebastian DiLorenzo","raw_affiliation_strings":["Department of Medical Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37"],"affiliations":[{"raw_affiliation_string":"Department of Medical Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041031533","display_name":"Johanna Sandgren","orcid":"https://orcid.org/0000-0001-6776-2649"},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I4210125936","display_name":"BioClinicum (Russia)","ror":"https://ror.org/02bw2gt68","country_code":"RU","type":"company","lineage":["https://openalex.org/I4210125936"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["RU","SE"],"is_corresponding":false,"raw_author_name":"Johanna Sandgren","raw_affiliation_strings":["Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164"],"affiliations":[{"raw_affiliation_string":"Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I4210125936","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022568973","display_name":"Teresita D\u00edaz de St\u00e5hl","orcid":"https://orcid.org/0000-0001-5933-6623"},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I4210125936","display_name":"BioClinicum (Russia)","ror":"https://ror.org/02bw2gt68","country_code":"RU","type":"company","lineage":["https://openalex.org/I4210125936"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["RU","SE"],"is_corresponding":false,"raw_author_name":"Teresita D\u00edaz De St\u00e5hl","raw_affiliation_strings":["Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164"],"affiliations":[{"raw_affiliation_string":"Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I4210125936","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035382345","display_name":"Philip Ewels","orcid":"https://orcid.org/0000-0003-4101-2502"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Philip Ewels","raw_affiliation_strings":["Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I161593684"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108562305","display_name":"Valtteri Wirta","orcid":null},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Valtteri Wirta","raw_affiliation_strings":["Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Facility, Science for Life Laboratory, Karolinska Institutet, Box 1031, Solna, 171 21"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Facility, Science for Life Laboratory, Karolinska Institutet, Box 1031, Solna, 171 21","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035824635","display_name":"Monica Nist\u00e9r","orcid":"https://orcid.org/0000-0002-1261-3790"},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I4210125936","display_name":"BioClinicum (Russia)","ror":"https://ror.org/02bw2gt68","country_code":"RU","type":"company","lineage":["https://openalex.org/I4210125936"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["RU","SE"],"is_corresponding":false,"raw_author_name":"Monica Nist\u00e9r","raw_affiliation_strings":["Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164"],"affiliations":[{"raw_affiliation_string":"Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I4210125936","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000356436","display_name":"Max K\u00e4ller","orcid":"https://orcid.org/0000-0001-6813-3051"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Max K\u00e4ller","raw_affiliation_strings":["School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, Solna, 17121"],"affiliations":[{"raw_affiliation_string":"School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, Solna, 17121","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I86987016"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020455782","display_name":"Bj\u00f6rn Nystedt","orcid":"https://orcid.org/0000-0001-7809-7664"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Bj\u00f6rn Nystedt","raw_affiliation_strings":["Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37"],"affiliations":[{"raw_affiliation_string":"Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I123387679"]}]}],"institution_assertions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1350,"currency":"USD","value_usd":1350,"provenance":"doaj"},"apc_paid":{"value":271,"currency":"EUR","value_usd":292,"provenance":"openapc"},"fwci":null,"has_fulltext":false,"cited_by_count":92,"citation_normalized_percentile":{"value":0.999326,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"9","issue":null,"first_page":"63","last_page":"63"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9991,"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":0.9991,"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":0.9976,"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":0.9941,"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":[],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7450025},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5573124},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5297614},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48988646},{"id":"https://openalex.org/C109825262","wikidata":"https://www.wikidata.org/wiki/Q1139164","display_name":"Germline","level":3,"score":0.4726319},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.45836127},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.45202848},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4268313},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4247249},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.41348064},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31569108},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2368029},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2205283},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1496551}],"mesh":[{"descriptor_ui":"D005854","descriptor_name":"Germ Cells","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.16665.1","pdf_url":"https://f1000researchdata.s3.amazonaws.com/manuscripts/18214/674fe691-deba-4c62-8c44-2a9f52b63f35_16665_-_bjorn_nystedt.pdf?doi=10.12688/f1000research.16665.1&numberOfBrowsableCollections=27&numberOfBrowsableInstitutionalCollections=5&numberOfBrowsableGateways=27","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":false,"landing_page_url":"https://doaj.org/article/73960a360a4448db9833dbe29df58531","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":true,"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":null,"is_accepted":false,"is_published":false},{"is_oa":true,"landing_page_url":"https://europepmc.org/articles/pmc7111497","pdf_url":"https://europepmc.org/articles/pmc7111497?pdf=render","source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":true,"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":["European Bioinformatics Institute"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-174221","pdf_url":"https://liu.diva-portal.org/smash/get/diva2:1537941/FULLTEXT01","source":{"id":"https://openalex.org/S4306400837","display_name":"DiVA (Linkoping University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://doi.org/10.1101/316976","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory"],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32269765","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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.16665.1","pdf_url":"https://f1000researchdata.s3.amazonaws.com/manuscripts/18214/674fe691-deba-4c62-8c44-2a9f52b63f35_16665_-_bjorn_nystedt.pdf?doi=10.12688/f1000research.16665.1&numberOfBrowsableCollections=27&numberOfBrowsableInstitutionalCollections=5&numberOfBrowsableGateways=27","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.52,"id":"https://metadata.un.org/sdg/9"}],"grants":[{"funder":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse","award_id":"2014.0278"},{"funder":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det","award_id":"2017-00630"},{"funder":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det","award_id":"2017-00656"},{"funder":"https://openalex.org/F4320323766","funder_display_name":"Barncancerfonden","award_id":"BB2019-0001"},{"funder":"https://openalex.org/F4320323766","funder_display_name":"Barncancerfonden","award_id":"BB2017-0001"},{"funder":"https://openalex.org/F4320323766","funder_display_name":"Barncancerfonden","award_id":"BB2018-0001"}],"datasets":[],"versions":[],"referenced_works_count":23,"referenced_works":["https://openalex.org/W2006288875","https://openalex.org/W2106578986","https://openalex.org/W2108234281","https://openalex.org/W2111281047","https://openalex.org/W2119180969","https://openalex.org/W2121743948","https://openalex.org/W2138601221","https://openalex.org/W2149992227","https://openalex.org/W2150131459","https://openalex.org/W2152956782","https://openalex.org/W2173033037","https://openalex.org/W2192272998","https://openalex.org/W2235737683","https://openalex.org/W2417483443","https://openalex.org/W2432815617","https://openalex.org/W2605897695","https://openalex.org/W2613409207","https://openalex.org/W2613764233","https://openalex.org/W2765745983","https://openalex.org/W2802080790","https://openalex.org/W2867868648","https://openalex.org/W2936909249","https://openalex.org/W4394666350"],"related_works":["https://openalex.org/W2625833328","https://openalex.org/W2392921965","https://openalex.org/W2377979023","https://openalex.org/W2361861616","https://openalex.org/W2358755282","https://openalex.org/W2263699433","https://openalex.org/W2218034408","https://openalex.org/W1990022233","https://openalex.org/W1533177136","https://openalex.org/W1481440753"],"abstract_inverted_index":{"Whole-genome":[0],"sequencing":[1,53,58,187],"(WGS)":[2],"is":[3,90],"a":[4,26,136,183,191],"fundamental":[5],"technology":[6],"for":[7,22,29,112,129,141,195],"research":[8,31,197],"to":[9,44],"advance":[10],"precision":[11],"medicine,":[12],"but":[13],"the":[14,93,125,142],"limited":[15],"availability":[16],"of":[17,139,146],"portable":[18],"and":[19,33,48,80,83,97,101,119,132,134,144,148,153,161,165,172,176,189,204,215],"user-friendly":[20],"workflows":[21],"WGS":[23,174],"analyses":[24],"poses":[25],"major":[27],"challenge":[28],"many":[30],"groups":[32],"hampers":[34],"scientific":[35],"progress.":[36],"Here":[37],"we":[38],"present":[39],"Sarek,":[40],"an":[41],"open-source":[42],"workflow":[43,95,185],"detect":[45],"germline":[46,147],"variants":[47],"somatic":[49,149],"mutations":[50],"based":[51],"on":[52,115],"data":[54],"from":[55],"WGS,":[56],"whole-exome":[57],"(WES),":[59],"or":[60],"gene":[61],"panels.":[62],"Sarek":[63,89,123,168,200],"features":[64],"(i)":[65],"easy":[66,113],"installation,":[67],"(ii)":[68],"robust":[69],"portability":[70],"across":[71],"different":[72],"computer":[73],"environments,":[74,108],"(iii)":[75],"comprehensive":[76],"documentation,":[77],"(iv)":[78],"transparent":[79],"easy-to-read":[81],"code,":[82,202],"(v)":[84],"extensive":[85],"quality":[86],"metrics":[87],"reporting.":[88],"implemented":[91],"in":[92,163],"Nextflow":[94],"language":[96],"supports":[98],"both":[99,181],"Docker":[100],"Singularity":[102],"containers":[103],"as":[104,106,182,190],"well":[105],"Conda":[107],"making":[109],"it":[110],"ideal":[111],"deployment":[114],"any":[116],"POSIX-compatible":[117],"computers":[118],"cloud":[120],"compute":[121],"environments.":[122],"follows":[124],"GATK":[126],"best-practice":[127],"recommendations":[128],"read":[130],"alignment":[131],"pre-processing,":[133],"includes":[135],"wide":[137],"range":[138],"software":[140],"identification":[143],"annotation":[145],"single-nucleotide":[150],"variants,":[151,155,157],"insertion":[152],"deletion":[154],"structural":[156],"tumour":[158],"sample":[159],"purity,":[160],"variations":[162],"ploidy":[164],"copy":[166],"number.":[167],"offers":[169],"easy,":[170],"efficient,":[171],"reproducible":[173],"analyses,":[175],"can":[177],"readily":[178],"be":[179],"used":[180],"production":[184],"at":[186,210,216],"facilities":[188],"powerful":[192],"stand-alone":[193],"tool":[194],"individual":[196],"groups.":[198],"The":[199],"source":[201],"documentation":[203],"installation":[205],"instructions":[206],"are":[207],"freely":[208],"available":[209],"https://github.com/nf-core/sarek":[214],"ns3:href=\"https://nf-co.re/sarek/\">https://nf-co.re/sarek/.":[220]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W4252335603","counts_by_year":[{"year":2024,"cited_by_count":32},{"year":2023,"cited_by_count":30},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1}],"updated_date":"2025-01-19T10:40:10.610058","created_date":"2022-05-12"}