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For: Spies N, Zook JM, Salit M, Sidow A. svviz: a read viewer for validating structural variants. Bioinformatics 2015;31:3994-6. [PMID: 26286809 DOI: 10.1093/bioinformatics/btv478] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/10/2015] [Indexed: 12/14/2022]  Open
Number Cited by Other Article(s)
1
Zhao S, Nakken S, Vodak D, Hovig E. FuSViz-visualization and interpretation of structural variation using cancer genomics and transcriptomics data. Nucleic Acids Res 2025;53:gkaf078. [PMID: 39995037 PMCID: PMC11850231 DOI: 10.1093/nar/gkaf078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 01/05/2025] [Accepted: 01/29/2025] [Indexed: 02/26/2025]  Open
2
Linderman MD, Wallace J, van der Heyde A, Wieman E, Brey D, Shi Y, Hansen P, Shamsi Z, Liu J, Gelb BD, Bashir A. NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data. Bioinformatics 2024;40:btae129. [PMID: 38444093 PMCID: PMC10955255 DOI: 10.1093/bioinformatics/btae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/15/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024]  Open
3
Lecomte L, Árnyasi M, Ferchaud A, Kent M, Lien S, Stenløkk K, Sylvestre F, Bernatchez L, Mérot C. Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations. Evol Appl 2024;17:e13653. [PMID: 38495945 PMCID: PMC10940791 DOI: 10.1111/eva.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/14/2023] [Accepted: 01/13/2024] [Indexed: 03/19/2024]  Open
4
Ahsan MU, Liu Q, Perdomo JE, Fang L, Wang K. A survey of algorithms for the detection of genomic structural variants from long-read sequencing data. Nat Methods 2023;20:1143-1158. [PMID: 37386186 PMCID: PMC11208083 DOI: 10.1038/s41592-023-01932-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
5
Dolzhenko E, Weisburd B, Ibañez K, Rajan-Babu IS, Anyansi C, Bennett MF, Billingsley K, Carroll A, Clamons S, Danzi MC, Deshpande V, Ding J, Fazal S, Halman A, Jadhav B, Qiu Y, Richmond PA, Saunders CT, Scheffler K, van Vugt JJFA, Zwamborn RRAJ, Genomics England Research Consortium, Chong SS, Friedman JM, Tucci A, Rehm HL, Eberle MA. REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats. Genome Med 2022;14:84. [PMID: 35948990 PMCID: PMC9367089 DOI: 10.1186/s13073-022-01085-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 07/11/2022] [Indexed: 01/28/2023]  Open
6
Linderman MD, Paudyal C, Shakeel M, Kelley W, Bashir A, Gelb BD. NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data. Gigascience 2021;10:giab046. [PMID: 34195837 PMCID: PMC8246072 DOI: 10.1093/gigascience/giab046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/04/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022]  Open
7
Belyeu JR, Chowdhury M, Brown J, Pedersen BS, Cormier MJ, Quinlan AR, Layer RM. Samplot: a platform for structural variant visual validation and automated filtering. Genome Biol 2021;22:161. [PMID: 34034781 PMCID: PMC8145817 DOI: 10.1186/s13059-021-02380-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 05/10/2021] [Indexed: 12/15/2022]  Open
8
Nattestad M, Aboukhalil R, Chin CS, Schatz MC. Ribbon: intuitive visualization for complex genomic variation. Bioinformatics 2021;37:413-415. [PMID: 32766814 DOI: 10.1093/bioinformatics/btaa680] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 06/15/2020] [Accepted: 07/21/2020] [Indexed: 01/08/2023]  Open
9
Minoche AE, Lundie B, Peters GB, Ohnesorg T, Pinese M, Thomas DM, Zankl A, Roscioli T, Schonrock N, Kummerfeld S, Burnett L, Dinger ME, Cowley MJ. ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data. Genome Med 2021;13:32. [PMID: 33632298 PMCID: PMC7908648 DOI: 10.1186/s13073-021-00841-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/02/2021] [Indexed: 01/09/2023]  Open
10
Zhou X, Zhang L, Weng Z, Dill DL, Sidow A. Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked reads. Nat Commun 2021;12:1077. [PMID: 33597536 PMCID: PMC7889865 DOI: 10.1038/s41467-021-21395-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 01/20/2021] [Indexed: 01/19/2023]  Open
11
Chu S, Skidmore ZL, Kunisaki J, Walker JR, Griffith M, Griffith OL, Bryan JN. Unraveling the chaotic genomic landscape of primary and metastatic canine appendicular osteosarcoma with current sequencing technologies and bioinformatic approaches. PLoS One 2021;16:e0246443. [PMID: 33556121 PMCID: PMC7870011 DOI: 10.1371/journal.pone.0246443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/19/2021] [Indexed: 12/03/2022]  Open
12
Cyrius: accurate CYP2D6 genotyping using whole-genome sequencing data. THE PHARMACOGENOMICS JOURNAL 2021;21:251-261. [PMID: 33462347 PMCID: PMC7997805 DOI: 10.1038/s41397-020-00205-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/13/2020] [Accepted: 12/04/2020] [Indexed: 12/03/2022]
13
Zarate S, Carroll A, Mahmoud M, Krasheninina O, Jun G, Salerno WJ, Schatz MC, Boerwinkle E, Gibbs RA, Sedlazeck FJ. Parliament2: Accurate structural variant calling at scale. Gigascience 2020;9:giaa145. [PMID: 33347570 PMCID: PMC7751401 DOI: 10.1093/gigascience/giaa145] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/17/2020] [Accepted: 11/18/2020] [Indexed: 12/24/2022]  Open
14
Chapman LM, Spies N, Pai P, Lim CS, Carroll A, Narzisi G, Watson CM, Proukakis C, Clarke WE, Nariai N, Dawson E, Jones G, Blankenberg D, Brueffer C, Xiao C, Kolora SRR, Alexander N, Wolujewicz P, Ahmed AE, Smith G, Shehreen S, Wenger AM, Salit M, Zook JM. A crowdsourced set of curated structural variants for the human genome. PLoS Comput Biol 2020;16:e1007933. [PMID: 32559231 PMCID: PMC7329145 DOI: 10.1371/journal.pcbi.1007933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 07/01/2020] [Accepted: 05/07/2020] [Indexed: 11/19/2022]  Open
15
Uguen K, Jubin C, Duffourd Y, Bardel C, Malan V, Dupont JM, El Khattabi L, Chatron N, Vitobello A, Rollat-Farnier PA, Baulard C, Lelorch M, Leduc A, Tisserant E, Tran Mau-Them F, Danjean V, Delepine M, Till M, Meyer V, Lyonnet S, Mosca-Boidron AL, Thevenon J, Faivre L, Thauvin-Robinet C, Schluth-Bolard C, Boland A, Olaso R, Callier P, Romana S, Deleuze JF, Sanlaville D. Genome sequencing in cytogenetics: Comparison of short-read and linked-read approaches for germline structural variant detection and characterization. Mol Genet Genomic Med 2020;8:e1114. [PMID: 31985172 PMCID: PMC7057128 DOI: 10.1002/mgg3.1114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022]  Open
16
Yokoyama TT, Kasahara M. Visualization tools for human structural variations identified by whole-genome sequencing. J Hum Genet 2020;65:49-60. [PMID: 31666648 PMCID: PMC8075883 DOI: 10.1038/s10038-019-0687-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/27/2019] [Accepted: 10/02/2019] [Indexed: 01/02/2023]
17
Zhang L, Zhou X, Weng Z, Sidow A. De novo diploid genome assembly for genome-wide structural variant detection. NAR Genom Bioinform 2019;2:lqz018. [PMID: 33575568 PMCID: PMC7671403 DOI: 10.1093/nargab/lqz018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/09/2019] [Accepted: 12/02/2019] [Indexed: 12/30/2022]  Open
18
Yokoyama TT, Sakamoto Y, Seki M, Suzuki Y, Kasahara M. MoMI-G: modular multi-scale integrated genome graph browser. BMC Bioinformatics 2019;20:548. [PMID: 31690272 PMCID: PMC6833150 DOI: 10.1186/s12859-019-3145-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/09/2019] [Indexed: 01/30/2023]  Open
19
Li D, Kim W, Wang L, Yoon KA, Park B, Park C, Kong SY, Hwang Y, Baek D, Lee ES, Won S. Comparison of INDEL Calling Tools with Simulation Data and Real Short-Read Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019;16:1635-1644. [PMID: 30004886 DOI: 10.1109/tcbb.2018.2854793] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
20
Hanlon K, Thompson A, Pantano L, Hutchinson JN, Al-Obeidi A, Wang S, Bliss-Moreau M, Helble J, Alexe G, Stegmaier K, Bauer DE, Croker BA. Single-cell cloning of human T-cell lines reveals clonal variation in cell death responses to chemotherapeutics. Cancer Genet 2019;237:69-77. [PMID: 31447068 DOI: 10.1016/j.cancergen.2019.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/18/2019] [Accepted: 06/09/2019] [Indexed: 12/12/2022]
21
Belyeu JR, Nicholas TJ, Pedersen BS, Sasani TA, Havrilla JM, Kravitz SN, Conway ME, Lohman BK, Quinlan AR, Layer RM. SV-plaudit: A cloud-based framework for manually curating thousands of structural variants. Gigascience 2018;7:5026174. [PMID: 29860504 PMCID: PMC6030999 DOI: 10.1093/gigascience/giy064] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/25/2018] [Indexed: 01/21/2023]  Open
22
Gross AM, Ajay SS, Rajan V, Brown C, Bluske K, Burns NJ, Chawla A, Coffey AJ, Malhotra A, Scocchia A, Thorpe E, Dzidic N, Hovanes K, Sahoo T, Dolzhenko E, Lajoie B, Khouzam A, Chowdhury S, Belmont J, Roller E, Ivakhno S, Tanner S, McEachern J, Hambuch T, Eberle M, Hagelstrom RT, Bentley DR, Perry DL, Taft RJ. Copy-number variants in clinical genome sequencing: deployment and interpretation for rare and undiagnosed disease. Genet Med 2018;21:1121-1130. [PMID: 30293986 PMCID: PMC6752263 DOI: 10.1038/s41436-018-0295-y] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/28/2018] [Indexed: 11/17/2022]  Open
23
Ahdesmäki MJ, Chapman BA, Cingolani P, Hofmann O, Sidoruk A, Lai Z, Zakharov G, Rodichenko M, Alperovich M, Jenkins D, Carr TH, Stetson D, Dougherty B, Barrett JC, Johnson JH. Prioritisation of structural variant calls in cancer genomes. PeerJ 2017;5:e3166. [PMID: 28392986 PMCID: PMC5382922 DOI: 10.7717/peerj.3166] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/09/2017] [Indexed: 12/24/2022]  Open
24
Noll AC, Miller NA, Smith LD, Yoo B, Fiedler S, Cooley LD, Willig LK, Petrikin JE, Cakici J, Lesko J, Newton A, Detherage K, Thiffault I, Saunders CJ, Farrow EG, Kingsmore SF. Clinical detection of deletion structural variants in whole-genome sequences. NPJ Genom Med 2016;1:16026. [PMID: 29263817 PMCID: PMC5685307 DOI: 10.1038/npjgenmed.2016.26] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 12/13/2022]  Open
25
Parikh H, Mohiyuddin M, Lam HYK, Iyer H, Chen D, Pratt M, Bartha G, Spies N, Losert W, Zook JM, Salit M. svclassify: a method to establish benchmark structural variant calls. BMC Genomics 2016;17:64. [PMID: 26772178 PMCID: PMC4715349 DOI: 10.1186/s12864-016-2366-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 01/05/2016] [Indexed: 01/24/2023]  Open
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