Exploiting sparseness in de novo genome assembly
文献类型：期刊论文
| 作者 | Ye CX[*]1,2,3; Ma ZS4; Cannon CH5,6; Pop M[*]3; Yu DW[*]2,7 |
| 刊名 | BMC BIOINFORMATICS
 |
| 出版日期 | 2012 |
| 卷号 | 13期号:Suppl 6页码:S1 |
| 通讯作者 | cxy@umd.edu ; mpop@umiacs.umd.edu ; douglas.yu@uea.ac.uk |
| 英文摘要 | 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. |
| 收录类别 | SCI |
| 资助信息 | This work was supported in part by Yunnan Province, China [20080A001], and the Chinese Academy of Sciences [0902281081, KSCX2-YW-Z-1027, Y002731079], and also by the US National Science Foundation grant IIS-0812111. This article has been published as part of BMC Bioinformatics Volume 13 Supplement 6, 2012: Proceedings of the Second Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2012). The full contents of the supplement are available online at http://www. biomedcentral.com/bmcbioinformatics/supplements/13/S6. |
| 语种 | 英语 |
| 源URL | [http://159.226.149.26:8080/handle/152453/10815]  |
| 专题 | 昆明动物研究所_动物生态学研究中心 昆明动物研究所_遗传资源与进化国家重点实验室 昆明动物研究所_计算生物与生物信息学 |
| 作者单位 | 1.Ecology & Evolution of Plant-Animal Interaction Group, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303 China 2.Ecology, Conservation, and Environment Center; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China 3.Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA 4.Computational Biology and Medical Ecology Lab; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China 5.Ecological Evolution Group, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303 China 6.Department of Biological Sciences, Texas Tech University, Lubbock, TX 79410 USA. 7.School of Biological Sciences, University of East Anglia, Norwich, Norfolk NR47TJ UK |
| 推荐引用方式 GB/T 7714 | Ye CX[*],Ma ZS,Cannon CH,et al. Exploiting sparseness in de novo genome assembly[J]. BMC BIOINFORMATICS,2012,13(Suppl 6):S1. |
| APA | Ye CX[*],Ma ZS,Cannon CH,Pop M[*],&Yu DW[*].(2012).Exploiting sparseness in de novo genome assembly.BMC BIOINFORMATICS,13(Suppl 6),S1. |
| MLA | Ye CX[*],et al."Exploiting sparseness in de novo genome assembly".BMC BIOINFORMATICS 13.Suppl 6(2012):S1. |
入库方式： OAI收割
来源：昆明动物研究所
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