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SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read sequencing.

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Title: SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read sequencing.
Authors: Elrick H; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK., Sauer CM; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK., Espejo Valle-Inclan J; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK., Trevers K; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK.; Research Department of Pathology, University College London Cancer Institute, London, UK., Tanguy M; Genomics England, London, UK., Zumalave S; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK., De Noon S; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK.; Research Department of Pathology, University College London Cancer Institute, London, UK., Muyas F; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK., Cascão R; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal., Afonso A; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal., Rust AG; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK., Amary F; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK.; Research Department of Pathology, University College London Cancer Institute, London, UK., Tirabosco R; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK.; Research Department of Pathology, University College London Cancer Institute, London, UK., Giess A; Genomics England, London, UK., Freeman T; Genomics England, London, UK., Sosinsky A; Genomics England, London, UK., Piculell K; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA., Miller DT; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA., Faria CC; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.; Department of Neurosurgery, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal., Elgar G; Genomics England, London, UK., Flanagan AM; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK. a.flanagan@ucl.ac.uk.; Research Department of Pathology, University College London Cancer Institute, London, UK. a.flanagan@ucl.ac.uk., Cortes-Ciriano I; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK. icortes@ebi.ac.uk.; Wellcome Sanger Institute, Cambridge, UK. icortes@ebi.ac.uk.
Source: Nature methods [Nat Methods] 2025 Jul; Vol. 22 (7), pp. 1436-1446. Date of Electronic Publication: 2025 May 28.
Publication Type: Journal Article
Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE
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  Data: <searchLink fieldCode="AU" term="%22Elrick+H%22">Elrick H</searchLink>; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.<br /><searchLink fieldCode="AU" term="%22Sauer+CM%22">Sauer CM</searchLink>; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.<br /><searchLink fieldCode="AU" term="%22Espejo+Valle-Inclan+J%22">Espejo Valle-Inclan J</searchLink>; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.<br /><searchLink fieldCode="AU" term="%22Trevers+K%22">Trevers K</searchLink>; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK.; Research Department of Pathology, University College London Cancer Institute, London, UK.<br /><searchLink fieldCode="AU" term="%22Tanguy+M%22">Tanguy M</searchLink>; Genomics England, London, UK.<br /><searchLink fieldCode="AU" term="%22Zumalave+S%22">Zumalave S</searchLink>; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.<br /><searchLink fieldCode="AU" term="%22De+Noon+S%22">De Noon S</searchLink>; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK.; Research Department of Pathology, University College London Cancer Institute, London, UK.<br /><searchLink fieldCode="AU" term="%22Muyas+F%22">Muyas F</searchLink>; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.<br /><searchLink fieldCode="AU" term="%22Cascão+R%22">Cascão R</searchLink>; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.<br /><searchLink fieldCode="AU" term="%22Afonso+A%22">Afonso A</searchLink>; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.<br /><searchLink fieldCode="AU" term="%22Rust+AG%22">Rust AG</searchLink>; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.<br /><searchLink fieldCode="AU" term="%22Amary+F%22">Amary F</searchLink>; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK.; Research Department of Pathology, University College London Cancer Institute, London, UK.<br /><searchLink fieldCode="AU" term="%22Tirabosco+R%22">Tirabosco R</searchLink>; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK.; Research Department of Pathology, University College London Cancer Institute, London, UK.<br /><searchLink fieldCode="AU" term="%22Giess+A%22">Giess A</searchLink>; Genomics England, London, UK.<br /><searchLink fieldCode="AU" term="%22Freeman+T%22">Freeman T</searchLink>; Genomics England, London, UK.<br /><searchLink fieldCode="AU" term="%22Sosinsky+A%22">Sosinsky A</searchLink>; Genomics England, London, UK.<br /><searchLink fieldCode="AU" term="%22Piculell+K%22">Piculell K</searchLink>; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.<br /><searchLink fieldCode="AU" term="%22Miller+DT%22">Miller DT</searchLink>; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.<br /><searchLink fieldCode="AU" term="%22Faria+CC%22">Faria CC</searchLink>; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.; Department of Neurosurgery, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal.<br /><searchLink fieldCode="AU" term="%22Elgar+G%22">Elgar G</searchLink>; Genomics England, London, UK.<br /><searchLink fieldCode="AU" term="%22Flanagan+AM%22">Flanagan AM</searchLink>; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK. a.flanagan@ucl.ac.uk.; Research Department of Pathology, University College London Cancer Institute, London, UK. a.flanagan@ucl.ac.uk.<br /><searchLink fieldCode="AU" term="%22Cortes-Ciriano+I%22">Cortes-Ciriano I</searchLink>; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK. icortes@ebi.ac.uk.; Wellcome Sanger Institute, Cambridge, UK. icortes@ebi.ac.uk.
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  Data: <searchLink fieldCode="JN" term="%22101215604%22">Nature methods</searchLink> [Nat Methods] 2025 Jul; Vol. 22 (7), pp. 1436-1446. <i>Date of Electronic Publication: </i>2025 May 28.
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