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 SV representations of state-of-the-art SV callers. We contextualize these ambiguities theoretically as well as practically and propose a graph-based approach for resolving them. Our graph model unifies both genomic strands using the concept of skew-symmetry; it supports graph genomes in general and pan genomes in specific. Instances of our model are inferred directly from seeds instead of the commonly used alignments that conflict with various types of SV as reported here. For 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.

中文翻译：

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最先进的结构变量调用：概念上出了什么问题以及如何解决？

结构变异（SV）调用属于现代生物信息学的标准工具，用于识别和描述基因组的变化。最初，这项工作提出了几种复杂的基因组重排，揭示了最新的SV调用者的SV表示固有的概念歧义。我们在理论上和实践上都对这些歧义进行了背景介绍，并提出了一种基于图的方法来解决它们。我们的图模型使用倾斜对称的概念统一了两条基因组链。它支持一般的图基因组和特定的泛基因组。我们的模型实例是直接从种子推断的，而不是如此处报道的与各种SV类型冲突的常用比对。对于酵母基因组 我们实际上计算了我们的图模型的邻接矩阵，并证明它们可以就另一个基因组提供高度准确的描述。我们的方法的开源原型实现可通过MIT许可在https://github.com/ITBE-Lab/MA获得。