Plant Diversity ›› 2012, Vol. 34 ›› Issue (5): 487-501.DOI: 10.3724/SP.J.1143.2012.12084

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Comparing De Novo Transcriptome Assemblers Using Illumina RNASeq Reads

 ZhAO  Lei, Zachary  LARSONRABIN, CHEN  Si-Yun, GUO  Zhen-Hua   

  1. Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany,
    Chinese Academy of Sciences, Kunming  650201, China
  • Received:2012-06-01 Online:2012-10-25 Published:2012-06-19


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

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