基于Illumina RNASeq短序列的转录组从头组装软件比较与优化

doi:10.3724/SP.J.1143.2012.12084

摘要/Abstract

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。

关键词: 高通量, 二代测序, 转录组, 从头组装, 优化

Abstract:

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.

Key words: Highthroughput, NGS, Transcriptome, de novo assembly, Optimized

中图分类号:

Q 75

赵磊, Zachary LARSONRABIN, 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]. Plant Diversity, 2012, 34(5): 487-501.

ZhAO Lei, Zachary LARSONRABIN, CHEN Si-Yun, GUO Zhen-Hua. Comparing De Novo Transcriptome Assemblers Using Illumina RNASeq Reads[J]. Plant Diversity, 2012, 34(5): 487-501.

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