BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach

doi:10.1093/bioinformatics/bty020

CSpace > 系统科学研究所

	BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach
	Wang, Anqi 1,2; Wang, Zhanyu 1,2; Li, Zheng 1,2; Li, Lei M.1,2,3
	2018-06-15
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	34 期号:12 页码:2019-2028
摘要	Motivation: It is highly desirable to assemble genomes of high continuity and consistency at low cost. The current bottleneck of draft genome continuity using the second generation sequencing (SGS) reads is primarily caused by uncertainty among repetitive sequences. Even though the single-molecule real-time sequencing technology is very promising to overcome the uncertainty issue, its relatively high cost and error rate add burden on budget or computation. Many long-read assemblers take the overlap-layout-consensus (OLC) paradigm, which is less sensitive to sequencing errors, heterozygosity and variability of coverage. However, current assemblers of SGS data do not sufficiently take advantage of the OLC approach. Results: Aiming at minimizing uncertainty, the proposed method BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can (i) perform reference-assisted assembly based on the genome of a close species (ii) or improve the results of existing assemblies that are obtained based on short or long sequencing reads. The tests on two eukaryote genomes, a wild rice Oryza longistaminata and a parrot Melopsittacus undulatus, show that BAUM achieved substantial improvement on genome size and continuity. Besides, BAUM reconstructed a considerable amount of repetitive regions that failed to be assembled by existing short read assemblers. We also propose statistical approaches to control the uncertainty in different steps of BAUM.
DOI	10.1093/bioinformatics/bty020
语种	英语
资助项目	Strategic Priority Research Program of the Chinese Academy of Sciences[XDB13040600] ; National Natural Science Foundation of China[91530105] ; National Natural Science Foundation of China[91130008] ; National Center for Mathematics and Interdisciplinary Sciences of the CAS ; Key Laboratory of Systems and Control of the CAS
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000435461900006
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/30492
专题	系统科学研究所
通讯作者	Li, Lei M.
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Wang, Anqi,Wang, Zhanyu,Li, Zheng,et al. BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach[J]. BIOINFORMATICS,2018,34(12):2019-2028.
APA	Wang, Anqi,Wang, Zhanyu,Li, Zheng,&Li, Lei M..(2018).BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach.BIOINFORMATICS,34(12),2019-2028.
MLA	Wang, Anqi,et al."BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach".BIOINFORMATICS 34.12(2018):2019-2028.