{"id":"https://openalex.org/W2098131178","doi":"https://doi.org/10.1093/bioinformatics/btp383","title":"Swift: primary data analysis for the Illumina Solexa sequencing platform","display_name":"Swift: primary data analysis for the Illumina Solexa sequencing platform","publication_year":2009,"publication_date":"2009-06-23","ids":{"openalex":"https://openalex.org/W2098131178","doi":"https://doi.org/10.1093/bioinformatics/btp383","mag":"2098131178","pmid":"https://pubmed.ncbi.nlm.nih.gov/19549630"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp383","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp383","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/17/2194/48995300/bioinformatics_25_17_2194.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/17/2194/48995300/bioinformatics_25_17_2194.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007699018","display_name":"Nava Whiteford","orcid":null},"institutions":[{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210124175","display_name":"Center for Astrophysics Harvard & Smithsonian","ror":"https://ror.org/03c3r2d17","country_code":"US","type":"education","lineage":["https://openalex.org/I103187081","https://openalex.org/I136199984","https://openalex.org/I4210124175"]}],"countries":["AU","GB","US"],"is_corresponding":true,"raw_author_name":"Nava Whiteford","raw_affiliation_strings":["1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I2802476451","https://openalex.org/I4210124175","https://openalex.org/I241749","https://openalex.org/I196021976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054374928","display_name":"Tom Skelly","orcid":null},"institutions":[{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210124175","display_name":"Center for Astrophysics Harvard & Smithsonian","ror":"https://ror.org/03c3r2d17","country_code":"US","type":"education","lineage":["https://openalex.org/I103187081","https://openalex.org/I136199984","https://openalex.org/I4210124175"]}],"countries":["AU","GB","US"],"is_corresponding":false,"raw_author_name":"Tom Skelly","raw_affiliation_strings":["1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I2802476451","https://openalex.org/I4210124175","https://openalex.org/I241749","https://openalex.org/I196021976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036849769","display_name":"Christina Curtis","orcid":"https://orcid.org/0000-0003-0166-3802"},"institutions":[{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210124175","display_name":"Center for Astrophysics Harvard & Smithsonian","ror":"https://ror.org/03c3r2d17","country_code":"US","type":"education","lineage":["https://openalex.org/I103187081","https://openalex.org/I136199984","https://openalex.org/I4210124175"]}],"countries":["AU","GB","US"],"is_corresponding":false,"raw_author_name":"Christina Curtis","raw_affiliation_strings":["1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I2802476451","https://openalex.org/I4210124175","https://openalex.org/I241749","https://openalex.org/I196021976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015434839","display_name":"Matthew E. Ritchie","orcid":"https://orcid.org/0000-0002-7383-0609"},"institutions":[{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210124175","display_name":"Center for Astrophysics Harvard & Smithsonian","ror":"https://ror.org/03c3r2d17","country_code":"US","type":"education","lineage":["https://openalex.org/I103187081","https://openalex.org/I136199984","https://openalex.org/I4210124175"]}],"countries":["AU","GB","US"],"is_corresponding":false,"raw_author_name":"Matt E. Ritchie","raw_affiliation_strings":["1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I2802476451","https://openalex.org/I4210124175","https://openalex.org/I241749","https://openalex.org/I196021976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112231811","display_name":"Andrea L\u00f6hr","orcid":null},"institutions":[{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210124175","display_name":"Center for Astrophysics Harvard & Smithsonian","ror":"https://ror.org/03c3r2d17","country_code":"US","type":"education","lineage":["https://openalex.org/I103187081","https://openalex.org/I136199984","https://openalex.org/I4210124175"]}],"countries":["AU","GB","US"],"is_corresponding":false,"raw_author_name":"Andrea L\u00f6hr","raw_affiliation_strings":["1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I2802476451","https://openalex.org/I4210124175","https://openalex.org/I241749","https://openalex.org/I196021976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060691708","display_name":"Alexander Wait Zaranek","orcid":"https://orcid.org/0000-0002-0415-9655"},"institutions":[{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210124175","display_name":"Center for Astrophysics Harvard & Smithsonian","ror":"https://ror.org/03c3r2d17","country_code":"US","type":"education","lineage":["https://openalex.org/I103187081","https://openalex.org/I136199984","https://openalex.org/I4210124175"]}],"countries":["AU","GB","US"],"is_corresponding":false,"raw_author_name":"Alexander Wait Zaranek","raw_affiliation_strings":["1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I2802476451","https://openalex.org/I4210124175","https://openalex.org/I241749","https://openalex.org/I196021976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032702053","display_name":"Irina Abnizova","orcid":"https://orcid.org/0000-0002-8460-8210"},"institutions":[{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210124175","display_name":"Center for Astrophysics Harvard & Smithsonian","ror":"https://ror.org/03c3r2d17","country_code":"US","type":"education","lineage":["https://openalex.org/I103187081","https://openalex.org/I136199984","https://openalex.org/I4210124175"]}],"countries":["AU","GB","US"],"is_corresponding":false,"raw_author_name":"Irina Abnizova","raw_affiliation_strings":["1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I2802476451","https://openalex.org/I4210124175","https://openalex.org/I241749","https://openalex.org/I196021976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066869533","display_name":"Clive Brown","orcid":null},"institutions":[{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210124175","display_name":"Center for Astrophysics Harvard & Smithsonian","ror":"https://ror.org/03c3r2d17","country_code":"US","type":"education","lineage":["https://openalex.org/I103187081","https://openalex.org/I136199984","https://openalex.org/I4210124175"]}],"countries":["AU","GB","US"],"is_corresponding":false,"raw_author_name":"Clive Brown","raw_affiliation_strings":["1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 2 Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE, UK, 3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, 4 Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Cambridge, MA 02138 and 5 Harvard Medical School, Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I2802476451","https://openalex.org/I4210124175","https://openalex.org/I241749","https://openalex.org/I196021976"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5007699018"],"corresponding_institution_ids":["https://openalex.org/I196021976","https://openalex.org/I241749","https://openalex.org/I2802476451","https://openalex.org/I4210124175"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.3204,"has_fulltext":true,"cited_by_count":117,"citation_normalized_percentile":{"value":0.95116165,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"25","issue":"17","first_page":"2194","last_page":"2199"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9886999726295471,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9857000112533569,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/swift","display_name":"Swift","score":0.7493833303451538},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7252799272537231},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5496807098388672},{"id":"https://openalex.org/keywords/vendor","display_name":"Vendor","score":0.4877474904060364},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44162338972091675},{"id":"https://openalex.org/keywords/mac-os","display_name":"Mac OS","score":0.42615509033203125},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.41655024886131287},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.26521292328834534},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15761542320251465},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14385131001472473},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07871094346046448}],"concepts":[{"id":"https://openalex.org/C116188536","wikidata":"https://www.wikidata.org/wiki/Q17118377","display_name":"Swift","level":2,"score":0.7493833303451538},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7252799272537231},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5496807098388672},{"id":"https://openalex.org/C2777338717","wikidata":"https://www.wikidata.org/wiki/Q1762621","display_name":"Vendor","level":2,"score":0.4877474904060364},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44162338972091675},{"id":"https://openalex.org/C522133331","wikidata":"https://www.wikidata.org/wiki/Q43627","display_name":"Mac OS","level":3,"score":0.42615509033203125},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.41655024886131287},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.26521292328834534},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15761542320251465},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14385131001472473},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07871094346046448},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btp383","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp383","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/17/2194/48995300/bioinformatics_25_17_2194.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19549630","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19549630","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:jupiter.its.unimelb.edu.au:11343/256749","is_oa":true,"landing_page_url":"http://hdl.handle.net/11343/256749","pdf_url":"http://hdl.handle.net/11343/256749","source":{"id":"https://openalex.org/S4377196259","display_name":"Minerva Access (University of Melbourne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165779595","host_organization_name":"The University of Melbourne","host_organization_lineage":["https://openalex.org/I165779595"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:dash.harvard.edu:1/4621712","is_oa":true,"landing_page_url":"http://nrs.harvard.edu/urn-3:HUL.InstRepos:4621712","pdf_url":null,"source":{"id":"https://openalex.org/S4306401540","display_name":"Digital Access to Scholarship at Harvard (DASH) (Harvard University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I136199984","host_organization_name":"Harvard University","host_organization_lineage":["https://openalex.org/I136199984"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.332.704","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.332.704","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2009/06/23/bioinformatics.btp383.full.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2734321","is_oa":true,"landing_page_url":"http://doi.org/10.1093/bioinformatics/btp383","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp383","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp383","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/17/2194/48995300/bioinformatics_25_17_2194.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2098131178.pdf","grobid_xml":"https://content.openalex.org/works/W2098131178.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1501775686","https://openalex.org/W1732678945","https://openalex.org/W1963943638","https://openalex.org/W1969454651","https://openalex.org/W2012016911","https://openalex.org/W2039716761","https://openalex.org/W2085060961","https://openalex.org/W2096070062","https://openalex.org/W2097812771","https://openalex.org/W2119274294","https://openalex.org/W2119923823","https://openalex.org/W2121016876","https://openalex.org/W2151732271","https://openalex.org/W2164216268","https://openalex.org/W2164741953","https://openalex.org/W6637825322","https://openalex.org/W6674437302"],"related_works":["https://openalex.org/W3198734187","https://openalex.org/W3175001965","https://openalex.org/W2350024083","https://openalex.org/W4250183494","https://openalex.org/W3130985054","https://openalex.org/W608019500","https://openalex.org/W3130134152","https://openalex.org/W2478736918","https://openalex.org/W3198661659","https://openalex.org/W3212027642"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Primary":[2],"data":[3,65,166],"analysis":[4,30,66,88],"methods":[5,16],"are":[6,167],"of":[7,48,79],"critical":[8],"importance":[9],"in":[10,134],"second":[11],"generation":[12],"DNA":[13],"sequencing.":[14],"Improved":[15],"have":[17],"the":[18,25,33,37,44,68,75,80,86,108,153],"potential":[19],"to":[20,35,94,119,150],"increase":[21,120],"yield":[22,121],"and":[23,46,104,129],"reduce":[24],"error":[26,126],"rates.":[27],"Openly":[28],"documented":[29],"tools":[31],"enable":[32],"user":[34],"understand":[36],"primary":[38,64],"data,":[39],"this":[40,54],"is":[41,74,117,132,140,156],"important":[42],"for":[43,62],"optimization":[45],"validity":[47],"their":[49],"scientific":[50],"work.":[51],"Results:":[52],"In":[53],"article,":[55],"we":[56],"describe":[57],"Swift,":[58],"a":[59],"new":[60],"tool":[61],"performing":[63],"on":[67],"Illumina":[69],"Solexa":[70],"Sequencing":[71],"Platform.":[72],"Swift":[73,116,131,155],"first":[76],"tool,":[77],"outside":[78],"vendors":[81],"own":[82],"software,":[83],"which":[84],"completes":[85],"full":[87],"process,":[89],"from":[90,158],"raw":[91],"images":[92],"through":[93],"base":[95],"calls.":[96],"As":[97],"such":[98],"it":[99],"provides":[100],"an":[101,143],"alternative":[102],"to,":[103],"independent":[105],"validation":[106],"of,":[107],"vendor":[109],"supplied":[110,141],"tool.":[111],"Our":[112],"results":[113],"show":[114],"that":[115],"able":[118],"by":[122],"13.8%,":[123],"at":[124,169],"comparable":[125],"rate.":[127],"Availability":[128],"Implementation:":[130],"implemented":[133],"C++and":[135],"supported":[136],"under":[137,142],"Linux.":[138],"It":[139],"open":[144],"source":[145],"license":[146],"(LGPL3),":[147],"allowing":[148],"researchers":[149],"build":[151],"upon":[152],"platform.":[154],"available":[157,168],"http://swiftng.sourceforge.net.":[159],"Contact:":[160],"new@sgenomics.org;":[161],"nava.whiteford@nanoporetech.com":[162],"Supplementary":[163,165],"information:":[164],"Bioinformatics":[170],"online.":[171]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":23},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":8}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
