Paper Info
Title
An External-Memory Algorithm for String Graph Construction
Abstract
Some recent results (Bauer et al. in Algorithms in bioinformatics, Springer, Berlin, pp 326---337, 2012; Cox et al. in Algorithms in bioinformatics, Springer, Berlin, pp. 214---224, 2012; Rosone and Sciortino in The nature of computation. Logic, algorithms, applications, Springer, Berlin, pp 353---364, 2013) have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows---Wheeler transform of the input strings. The motivations for those results stem from Bioinformatics, where a large number of short strings (called reads) are routinely produced and analyzed. In that field, a fundamental problem is to assemble a genome from a large set of much shorter samples extracted from the unknown genome. The approaches that are currently used to tackle this problem are memory-intensive. This fact does not bode well with the ongoing increase in the availability of genomic data. A data structure that is used in genome assembly is the string graph, where vertices correspond to samples and arcs represent two overlapping samples. In this paper we address an open problem of Simpson and Durbin (Bioinformatics 26(12):i367---i373, 2010): to design an external-memory algorithm to compute the string graph.
Year
DOI
Venue
2017
10.1007/s00453-016-0165-4
Algorithmica
Keywords
Field
DocType
External memory algorithms,Burrows–Wheeler transform,String graphs,Genome assembly
Genome,String searching algorithm,Data structure,Combinatorics,Open problem,Vertex (geometry),Computer science,Algorithm,String graph,Theoretical computer science,Sequence assembly,Auxiliary memory
Journal
Volume
Issue
ISSN
78
2
0178-4617
Citations 
PageRank 
References 
3
0.38
25
Authors
5
Name
Order
Citations
PageRank
Paola Bonizzoni150252.23
Gianluca Della Vedova234236.39
Yuri Pirola312815.79
Marco Previtali4225.45
Raffaella Rizzi513013.58