MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from readsopen access
- Authors
- Schmidt, Markus; Kutzner, Arne
- Issue Date
- Jul-2023
- Publisher
- BMC
- Keywords
- Nested SV; Complex SV; Alignment; MEMs; Seeds; Pan-genomes; Ambiguity
- Citation
- GENOME BIOLOGY, v.24, no.1, pp.1 - 27
- Indexed
- SCIE
SCOPUS
- Journal Title
- GENOME BIOLOGY
- Volume
- 24
- Number
- 1
- Start Page
- 1
- End Page
- 27
- URI
- https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/189658
- DOI
- 10.1186/s13059-023-03009-5
- ISSN
- 1474-7596
- 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 .
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Collections - 서울 공과대학 > 서울 정보시스템학과 > 1. Journal Articles
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