MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
Abstract Structural variant (SV) calling belongs to the standard tools of modern bioinformatics for identifying and describing alterations in genomes. Initially, this work presents several complex genomic rearrangements that reveal conceptual ambiguities inherent to the representation via basic SV....
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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BMC
2023-07-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-023-03009-5 |
| _version_ | 1797774158380138496 |
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| author | Markus Schmidt Arne Kutzner |
| author_facet | Markus Schmidt Arne Kutzner |
| author_sort | Markus Schmidt |
| collection | DOAJ |
| description | Abstract Structural variant (SV) calling belongs to the standard tools of modern bioinformatics for identifying and describing alterations in genomes. Initially, this work presents several complex genomic rearrangements that reveal conceptual ambiguities inherent to the representation via basic SV. We contextualize these ambiguities theoretically as well as practically and propose a graph-based approach for resolving them. For various yeast genomes, we practically compute adjacency matrices of our graph model and demonstrate that they provide highly accurate descriptions of one genome in terms of another. An open-source prototype implementation of our approach is available under the MIT license at https://github.com/ITBE-Lab/MA . |
| first_indexed | 2024-03-12T22:16:53Z |
| format | Article |
| id | doaj.art-70781a912727432d9b074e6211c249e8 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-03-12T22:16:53Z |
| publishDate | 2023-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-70781a912727432d9b074e6211c249e82023-07-23T11:15:57ZengBMCGenome Biology1474-760X2023-07-0124112710.1186/s13059-023-03009-5MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from readsMarkus Schmidt0Arne Kutzner1Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-UniversitätDepartment of Information Systems, College of Engineering, Hanyang UniversityAbstract Structural variant (SV) calling belongs to the standard tools of modern bioinformatics for identifying and describing alterations in genomes. Initially, this work presents several complex genomic rearrangements that reveal conceptual ambiguities inherent to the representation via basic SV. We contextualize these ambiguities theoretically as well as practically and propose a graph-based approach for resolving them. For various yeast genomes, we practically compute adjacency matrices of our graph model and demonstrate that they provide highly accurate descriptions of one genome in terms of another. An open-source prototype implementation of our approach is available under the MIT license at https://github.com/ITBE-Lab/MA .https://doi.org/10.1186/s13059-023-03009-5Nested SVComplex SVAlignmentMEMsSeedsPan-genomes |
| spellingShingle | Markus Schmidt Arne Kutzner MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads Genome Biology Nested SV Complex SV Alignment MEMs Seeds Pan-genomes |
| title | MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads |
| title_full | MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads |
| title_fullStr | MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads |
| title_full_unstemmed | MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads |
| title_short | MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads |
| title_sort | msv a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads |
| topic | Nested SV Complex SV Alignment MEMs Seeds Pan-genomes |
| url | https://doi.org/10.1186/s13059-023-03009-5 |
| work_keys_str_mv | AT markusschmidt msvamodularstructuralvariantcallerthatrevealsnestedandcomplexrearrangementsbyunifyingbreakendsinferreddirectlyfromreads AT arnekutzner msvamodularstructuralvariantcallerthatrevealsnestedandcomplexrearrangementsbyunifyingbreakendsinferreddirectlyfromreads |