An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals

doi:10.1098/rsos.171589

	An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals
	Li, Yu-Long1,2 ; Xue, Dong-Xiu1,2 ; Zhang, Bai-Dong1,2 ; Liu, Jin-Xian 1,2
	2018-02-01
发表期刊	ROYAL SOCIETY OPEN SCIENCE
ISSN	2054-5703
卷号	5 期号:2 页码:11
通讯作者	Liu, Jin-Xian(jinxianliu@gmail.com)
摘要	Restriction site-associated DNA (RAD) sequencing is revolutionizing studies in ecological, evolutionary and conservation genomics. However, the assembly of paired-end RAD reads with random-sheared ends is still challenging, especially for non-model species with high genetic variance. Here, we present an efficient optimized approach with a pipeline software, RADassembler, which makes full use of paired-end RAD reads with random-sheared ends from multiple individuals to assemble RAD contigs. RADassembler integrates the algorithms for choosing the optimal number of mismatches within and across individuals at the clustering stage, and then uses a two-step assembly approach at the assembly stage. RADassembler also uses data reduction and parallelization strategies to promote efficiency. Compared to other tools, both the assembly results based on simulation and real RAD datasets demonstrated that RADassembler could always assemble the appropriate number of contigs with high qualities, and more read pairs were properly mapped to the assembled contigs. This approach provides an optimal tool for dealing with the complexity in the assembly of paired-end RAD reads with random-sheared ends for non-model species in ecological, evolutionary and conservation studies.
关键词	overlapping paired-end sequencing RAD-seq optimized assembly pipeline software optimal clustering
DOI	10.1098/rsos.171589
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China (NSFC)[41676137] ; National Natural Science Foundation of China (NSFC)[31502169] ; AoShan Talents Program Qingdao National Laboratory for Marine Science and Technology[2015ASTP-ES05] ; NSFC-Shandong Joint Fund for Marine Ecology and Environmental Sciences[U1606404] ; National Natural Science Foundation of China (NSFC)[41676137] ; National Natural Science Foundation of China (NSFC)[31502169] ; AoShan Talents Program Qingdao National Laboratory for Marine Science and Technology[2015ASTP-ES05] ; NSFC-Shandong Joint Fund for Marine Ecology and Environmental Sciences[U1606404]
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000426465700055
出版者	ROYAL SOC
引用统计	被引频次：6[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/157601
专题	海洋生态与环境科学重点实验室
通讯作者	Liu, Jin-Xian
作者单位	1.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, 7 Nanhai Rd, Qingdao 266071, Shandong, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao 266071, Peoples R China
第一作者单位	中国科学院海洋研究所
通讯作者单位	中国科学院海洋研究所
推荐引用方式 GB/T 7714	Li, Yu-Long,Xue, Dong-Xiu,Zhang, Bai-Dong,et al. An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals[J]. ROYAL SOCIETY OPEN SCIENCE,2018,5(2):11.
APA	Li, Yu-Long,Xue, Dong-Xiu,Zhang, Bai-Dong,&Liu, Jin-Xian.(2018).An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals.ROYAL SOCIETY OPEN SCIENCE,5(2),11.
MLA	Li, Yu-Long,et al."An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals".ROYAL SOCIETY OPEN SCIENCE 5.2(2018):11.

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