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An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals
Li, Yu-Long; Xue, Dong-Xiu; Zhang, Bai-Dong; Liu, Jin-Xian
2018-02-01
Source PublicationROYAL SOCIETY OPEN SCIENCE
ISSN2054-5703
Volume5Issue:2
SubtypeArticle
AbstractRestriction 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.
Keywordoverlapping paired-end sequencing RAD-seq optimized assembly pipeline software optimal clustering
Subject AreaScience & Technology - Other Topics
DOI10.1098/rsos.171589
Indexed BySCIE
Language英语
WOS Research AreaMultidisciplinary Sciences
WOS IDWOS:000426465700055
PublisherROYAL SOC
Citation statistics
Cited Times:1[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/157601
Collection海洋生态与环境科学重点实验室
Affiliation1.[Li, Yu-Long
2.Xue, Dong-Xiu
3.Zhang, Bai-Dong
4.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, 7 Nanhai Rd, Qingdao 266071, Shandong, Peoples R China
5.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao 266071, Peoples R China
Recommended Citation
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).
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).
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).
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