Space Efficient Merging of de Bruijn Graphs and Wheeler Graphs

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 t...

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Vydáno v:Algorithmica Ročník 84; číslo 3; s. 639 - 669
Hlavní autoři: Egidi, Lavinia, Louza, Felipe A., Manzini, Giovanni
Médium: Journal Article
Jazyk:angličtina
Vydáno: New York Springer US 01.03.2022
Springer Nature B.V
Témata:
Algorithm Analysis and Problem Complexity
Algorithms
Asymptotic properties
Computer Science
Computer Systems Organization and Communication Networks
Data structures
Data Structures and Information Theory
Graph theory
Graphical representations
Graphs
Mathematics of Computing
Special Issue from London Stringology Days & London Algorithmic Workshop
Theory of Computation
Succinct data structures
Space efficient algorithms
de Bruijn graphs
Wheeler graphs
BWT variants
ISSN:0178-4617, 1432-0541
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Shrnutí: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.
Bibliografie:ObjectType-Article-1
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ISSN:0178-4617
1432-0541
DOI:10.1007/s00453-021-00855-2