Exploiting sparseness in de novo genome assembly

Ye, Chengxi, Ma, Zhanshan Sam, Cannon, Charles H., Pop, Mihai and Yu, Douglas W. (2012) Exploiting sparseness in de novo genome assembly. BMC Bioinformatics, 13 (Suppl 6). ISSN 1471-2105

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Abstract

Background: The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. Methods: In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k- mers as nodes and the links between these nodes allows the de novo assembly of even moderately-sized genomes (~500 M) on a typical laptop computer. Results: We implement this sparse graph concept in a proof-of-principle software package, SparseAssembler, utilizing a new sparse k- mer graph structure evolved from the de Bruijn graph. We test our SparseAssembler with both simulated and real data, achieving ~90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing de novo assemblers.

Item Type:	Article
Faculty \ School:	Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Organisms and the Environment
Depositing User:	Users 2731 not found.
Date Deposited:	03 Oct 2012 09:19
Last Modified:	14 May 2023 20:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/39740
DOI:	10.1186/1471-2105-13-S6-S1

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