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HaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome Assembly
Joint Authors
Rahman, M. Sohel
Rahman, Md Mahfuzer
Sharker, Ratul
Biswas, Sajib
Source
International Journal of Genomics
Issue
Vol. 2017, Issue 2017 (31 Dec. 2017), pp.1-12, 12 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2017-08-27
Country of Publication
Egypt
No. of Pages
12
Main Subjects
Abstract EN
Background.
The rapid advancement of sequencing technologies has made it possible to regularly produce millions of high-quality reads from the DNA samples in the sequencing laboratories.
To this end, the de Bruijn graph is a popular data structure in the genome assembly literature for efficient representation and processing of data.
Due to the number of nodes in a de Bruijn graph, the main barrier here is the memory and runtime.
Therefore, this area has received significant attention in contemporary literature.
Results.
In this paper, we present an approach called HaVec that attempts to achieve a balance between the memory consumption and the running time.
HaVec uses a hash table along with an auxiliary vector data structure to store the de Bruijn graph thereby improving the total memory usage and the running time.
A critical and noteworthy feature of HaVec is that it exhibits no false positive error.
Conclusions.
In general, the graph construction procedure takes the major share of the time involved in an assembly process.
HaVec can be seen as a significant advancement in this aspect.
We anticipate that HaVec will be extremely useful in the de Bruijn graph-based genome assembly.
American Psychological Association (APA)
Rahman, Md Mahfuzer& Sharker, Ratul& Biswas, Sajib& Rahman, M. Sohel. 2017. HaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome Assembly. International Journal of Genomics،Vol. 2017, no. 2017, pp.1-12.
https://search.emarefa.net/detail/BIM-1167161
Modern Language Association (MLA)
Rahman, Md Mahfuzer…[et al.]. HaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome Assembly. International Journal of Genomics No. 2017 (2017), pp.1-12.
https://search.emarefa.net/detail/BIM-1167161
American Medical Association (AMA)
Rahman, Md Mahfuzer& Sharker, Ratul& Biswas, Sajib& Rahman, M. Sohel. HaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome Assembly. International Journal of Genomics. 2017. Vol. 2017, no. 2017, pp.1-12.
https://search.emarefa.net/detail/BIM-1167161
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1167161