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Space Efficient Merging of de Bruijn Graphs and Wheeler Graphs
Algorithmica ( IF 1.1 ) Pub Date : 2021-07-16 , DOI: 10.1007/s00453-021-00855-2
Lavinia Egidi 1 , Felipe A. Louza 2 , Giovanni Manzini 3
Affiliation  

The merging of succinct data structures is a well established technique for the space efficient construction of large succinct indexes. In the first part of the paper we propose a new algorithm for merging succinct representations of de Bruijn graphs. Our algorithm has the same asymptotic cost of the state of the art algorithm for the same problem but it uses less than half of its working space. A novel important feature of our algorithm, not found in any of the existing tools, is that it can compute the Variable Order succinct representation of the union graph within the same asymptotic time/space bounds. In the second part of the paper we consider the more general problem of merging succinct representations of Wheeler graphs, a recently introduced graph family which includes as special cases de Bruijn graphs and many other known succinct indexes based on the BWT or one of its variants. In this paper we provide a space efficient algorithm for Wheeler graph merging; our algorithm works under the assumption that the union of the input Wheeler graphs has an ordering that satisfies the Wheeler conditions and which is compatible with the ordering of the original graphs.



中文翻译:

de Bruijn 图和惠勒图的空间高效合并

简洁数据结构的合并是一种行之有效的大型简洁索引的空间高效构建技术。在论文的第一部分,我们提出了一种新算法,用于合并de Bruijn 图的简洁表示。对于同一问题,我们的算法具有与最先进算法相同的渐近成本,但它使用的工作空间不到其一半。我们算法的一个新的重要特性是在任何现有工具中都没有发现的,它可以在相同的渐近时间/空间边界内计算联合图的可变阶简洁表示。在论文的第二部分,我们考虑了合并惠勒图的简洁表示的更一般问题,最近引入的图族,其中包括作为特例的 de Bruijn 图和许多其他已知的基于 BWT 或其变体的简洁索引。在本文中,我们为惠勒图合并提供了一种空间高效的算法;我们的算法假设输入惠勒图的并集具有满足惠勒条件的排序,并且与原始图的排序兼容。

更新日期:2021-07-16
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