IOCAS-IR  > 海洋生物技术研发中心
Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology
Song, Kai1,2,3; Li, Li1,2,3; Zhang, Guofan1,3,4
2016-10-20
发表期刊SCIENTIFIC REPORTS
卷号6
文章类型Article
摘要Next-generation sequencing (NGS) technology is being applied to an increasing number of non-model species and has been used as the primary approach for accurate genotyping in genetic and evolutionary studies. However, inferring genotypes from sequencing data is challenging, particularly for organisms with a high degree of heterozygosity. This is because genotype calls from sequencing data are often inaccurate due to low sequencing coverage, and if this is not accounted for, genotype uncertainty can lead to serious bias in downstream analyses, such as quantitative trait locus mapping and genome-wide association studies. Here, we used high-coverage reference data sets from Crassostrea gigas to simulate sequencing data with different coverage, and we evaluate the influence of genotype calling rate and accuracy as a function of coverage. Having initially identified the appropriate parameter settings for filtering to ensure genotype accuracy, we used two different single-nucleotide polymorphism (SNP) calling pipelines, single-sample and multi-sample. We found that a coverage of 15 x was suitable for obtaining sufficient numbers of SNPs with high accuracy. Our work provides guidelines for the selection of sequence coverage when using NGS to investigate species with a high degree of heterozygosity and rapid decay of linkage disequilibrium.
DOI10.1038/srep35736
收录类别SCI
语种英语
WOS记录号WOS:000386084200001
引用统计
被引频次:3[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
版本出版稿
条目标识符http://ir.qdio.ac.cn/handle/337002/136175
专题海洋生物技术研发中心
作者单位1.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Shandong, Peoples R China
2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Fisheries & Aquaculture, Qingdao 266071, Shandong, Peoples R China
3.Chinese Acad Sci, Inst Oceanol, Natl & Local Joint Engn Lab Ecol Mariculture, Qingdao 266071, Shandong, Peoples R China
4.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266071, Shandong, Peoples R China
推荐引用方式
GB/T 7714
Song, Kai,Li, Li,Zhang, Guofan. Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology[J]. SCIENTIFIC REPORTS,2016,6.
APA Song, Kai,Li, Li,&Zhang, Guofan.(2016).Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology.SCIENTIFIC REPORTS,6.
MLA Song, Kai,et al."Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology".SCIENTIFIC REPORTS 6(2016).
条目包含的文件
文件名称/大小 文献类型 版本类型 开放类型 使用许可
Coverage recommendat(633KB)期刊论文出版稿开放获取CC BY-NC-SA浏览 请求全文
个性服务
推荐该条目
保存到收藏夹
查看访问统计
导出为Endnote文件
谷歌学术
谷歌学术中相似的文章
[Song, Kai]的文章
[Li, Li]的文章
[Zhang, Guofan]的文章
百度学术
百度学术中相似的文章
[Song, Kai]的文章
[Li, Li]的文章
[Zhang, Guofan]的文章
必应学术
必应学术中相似的文章
[Song, Kai]的文章
[Li, Li]的文章
[Zhang, Guofan]的文章
相关权益政策
暂无数据
收藏/分享
文件名: Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology.pdf
格式: Adobe PDF
所有评论 (0)
暂无评论
 

除非特别说明,本系统中所有内容都受版权保护,并保留所有权利。