Exploiting sparseness in de novo genome assembly

Ye, Chengxi, Ma, Zhanshan Sam, Cannon, Charles H., Pop, Mihai and Yu, Douglas W. ORCID: https://orcid.org/0000-0001-8551-5609 (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:	18 Jun 2026 14:46
URI:	https://ueaeprints.uea.ac.uk/id/eprint/39740
DOI:	10.1186/1471-2105-13-S6-S1

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