HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies

doi:10.1093/nar/gkr354

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	HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies
	Kim, Jong Hyun 2,3; Kim, Woo-Cheol 1; Li, Lei M.4,5 ; Park, Sanghyun 1
	2011-07-01
发表期刊	NUCLEIC ACIDS RESEARCH
ISSN	0305-1048
卷号	39 页码:W557-W561
摘要	The massively parallel sequencing technologies have recently flourished and dramatically cut the cost to sequence personal human genomes. Haplotype assembly from personal genomes sequenced using the massively parallel sequencing technologies is becoming a cost-effective and promising tool for human disease study. Computational assembly of haplotypes has been proved to be very accurate, but obviously contains errors. Here we present a tool, HapEdit, to assess the accuracy of assembled haplotypes and edit them manually. Using this tool, a user can break erroneous haplotype segments into smaller segments, or concatenate haplotype segments if the concatenated haplotype segments are sufficiently supported. A user can also edit bases with low-quality scores. HapEdit displays haplotype assemblies so that a user can easily navigate and pinpoint a region of interest. As inputs, HapEdit currently takes reads from the Polonator, Illumina, SOLiD, 454 and Sanger sequencing technologies.
DOI	10.1093/nar/gkr354
语种	英语
资助项目	National Research Foundation of Korea[2009-0083311] ; National Research Foundation of Korea[2011-0004382] ; National Institutes of Health, USA[HG002790]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000292325300091
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/11675
专题	系统科学研究所
通讯作者	Park, Sanghyun
作者单位	1.Yonsei Univ, Dept Comp Sci, Seoul 120749, South Korea 2.Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA 3.Broad Inst MIT & Harvard, Cambridge, MA 02142 USA 4.Univ So Calif, Mol & Computat Biol Program, Dept Biol Sci, Los Angeles, CA 90089 USA 5.Chinese Acad Sci, Inst Syst Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Kim, Jong Hyun,Kim, Woo-Cheol,Li, Lei M.,et al. HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies[J]. NUCLEIC ACIDS RESEARCH,2011,39:W557-W561.
APA	Kim, Jong Hyun,Kim, Woo-Cheol,Li, Lei M.,&Park, Sanghyun.(2011).HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies.NUCLEIC ACIDS RESEARCH,39,W557-W561.
MLA	Kim, Jong Hyun,et al."HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies".NUCLEIC ACIDS RESEARCH 39(2011):W557-W561.