干旱区生态环境知识资源中心(Arid): 基于Illumina RNA-Seq短序列的转录组从头组装软件比较与优化

Arid

	基于Illumina RNA-Seq短序列的转录组从头组装软件比较与优化
其他题名	Comparing De Novo Transcriptome Assemblers Using Illumina RNA-Seq Reads
	赵磊; 陈斯云; 郭振华
来源期刊	植物分类与资源学报
ISSN	2095-0845
出版年	2012
卷号	34 期号:5 页码:487-501
中文摘要	利用公共数据库中果蝇F1代和栽培水稻基于高通量Illumina测序平台的RNA-Seq短序列数据,比较了8个(ABySS, Velvet, SOAPdenovo, Oases, Trinity, Multiple-k, T-IDBA and Trans-ABySS)转录组从头组装软件。结果显示,在基于单一k-mer和多重k-mer方法的两类软件中,Trinity和Trans-ABySS分别表现出最好的组装性能,而其它软件性能比较接近。我们还发现基于多重k-mer比单一k-mer可以组装获得更多的总碱基数目,但是即使利用最好的多重k-mer组装软件,所获得的数据质量也比研究人员所期望的要低。鉴于此,我们提出了"ETM"优化方法,将多重k-mer方法组合到Trinity中,使其在具有最好的组装性能的基础上兼具了多重k-mer的优势,测试结果显示了该方法具有一定的优越性。我们的研究结果为用户选择合适的软件提供了依据,对推动基于高通量Illumina测序的转录组研究具有重要意义。
英文摘要	In this study, we carried out a systematic comparison of the de novo transcriptome assembly performance of eight assemblers (ABySS, Velvet, SOAPdenovo, Oases, Trinity, Multiple-k, T-IDBA and Trans-ABySS), processing Illumina RNA-Seq reads from F1 hybrids (Drosophila MS) of Drosophila melanogaster and Drosophila sechellia and cultivated rice. Our study showed that Trinity and Trans-ABySS were the most effective for producing transcriptomes from our trial datasets using single k-mer and multiple k-mer methods, respectively, although the performance levels of the other tested assemblers were comparable. We found that using single k-mer assemblers generally produced fewer total numbers of bases than multiple k-mer assemblers, although even the best assembler’s results showed lower quality than some researchers may desire. Therefore, we developed and tested a novel de novo transcriptome assembly method, ETM, which employs a combination of multiple k-mer tools with Trinity assembler. The ETM method yielded superior results from our trial datasets. Our results will assist the growing number of transcriptome projects using Illumina RNA-Seq reads and provide guidelines for choosing appropriate software.
中文关键词	高通量 ; 二代测序 ; 转录组 ; 从头组装 ; 优化
英文关键词	High-throughput NGS Transcriptome de novo assembly Optimized
语种	英语
国家	中国
收录类别	CSCD
WOS类目	GENETICS HEREDITY
WOS研究方向	Genetics & Heredity
CSCD记录号	CSCD:4662827
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/228857
作者单位	Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
推荐引用方式 GB/T 7714	赵磊,陈斯云,郭振华. 基于Illumina RNA-Seq短序列的转录组从头组装软件比较与优化[J],2012,34(5):487-501.
APA	赵磊,陈斯云,&郭振华.(2012).基于Illumina RNA-Seq短序列的转录组从头组装软件比较与优化.植物分类与资源学报,34(5),487-501.
MLA	赵磊,et al."基于Illumina RNA-Seq短序列的转录组从头组装软件比较与优化".植物分类与资源学报 34.5(2012):487-501.