Exploiting sparseness in de novo genome assembly

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	Exploiting sparseness in de novo genome assembly
	Ye, Chengxi 2,3; Ma, Zhanshan Sam 4; Cannon, Charles H.; Pop, Mihai 2,3; Yu, Douglas W.
	2012
Conference Name	2nd Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq)
Source Publication	BMC BIOINFORMATICS
Volume	13
Pages	-
Conference Date	APR 19-20, 2012
Country	Barcelona, SPAIN
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 (similar to 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 similar to 90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing de novo assemblers.
Language	英语
Document Type	会议论文
Identifier	https://ir.xtbg.ac.cn/handle/353005/15128
Collection	版纳植物园会议文献
Affiliation	1.Chinese Acad Sci, Xishuangbanna Trop Bot Garden, Ecol & Evolut Plant Anim Interact Grp, Mengiun 666303, Yunnan, Peoples R China 2.Ye, Chengxi; Yu, Douglas W.] Chinese Acad Sci, Kunming Inst Zool, Ecol Conservat & Environm Ctr, State Key Lab Genet Resources & Evolut, Kunming 650223, Yunnan, Peoples R China 3.Univ Maryland, Dept Comp Sci, College Pk, MD 20742 USA 4.Univ Maryland, Inst Adv Comp Studies, Ctr Bioinformat & Computat Biol, College Pk, MD 20742 USA 5.Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Computat Biol & Med Ecol Lab, Kunming 650223, Yunnan, Peoples R China 6.Cannon, Charles H.] Chinese Acad Sci, Xishuangbanna Trop Bot Garden, Ecol Evolut Grp, Mengiun 666303, Yunnan, Peoples R China 7.Cannon, Charles H.] Texas Tech Univ, Dept Biol Sci, Lubbock, TX 79410 USA 8.Yu, Douglas W.] Univ E Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England
Recommended Citation GB/T 7714	Ye, Chengxi,Ma, Zhanshan Sam,Cannon, Charles H.,et al. Exploiting sparseness in de novo genome assembly[C],2012:-.

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