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基于马铃薯转录组数据的病毒组装软件比较
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Abstract:
随着高通量测序技术的成熟和成本的降低，转录组数据呈现爆发式增长。转录组数据中除了包含寄主马铃薯自身的转录本以外，还可能包含寄主受到RNA病毒侵染而带来的病毒序列信息，因此可以低成本地从转录组数据中进行病毒基因组挖掘。本研究通过比较SOAPdenovo、IDBA-UD、Trinity 三种主流软件对RNA-seq数据的组装效果，发现Trinity软件组装得到的结果中序列信息最丰富，且长序列最多，但组装过程耗时较长；相对而言，SOAPdenovo和IDBA-UD耗时较短，但组装结果中序列信息较少且长序列较少，所以推荐使用Trinity软件进行基于转录组数据的病毒基因组组装。
With the continuous maturity of high-throughput sequencing technology and the reduction of cost, transcriptome data show explosive growth. The potato transcriptome data not only contains the transcripts of the potato itself, but also contains the viral sequence information caused by the infection of viruses in the sample, so the virus genome mining can be carried out from the transcriptome data. In this study, the assembly results of three mainstream software (SOAPdenovo, IDBA-UD and Trinity3) were compared based on the same RNA-seq data, it was found that Trinity software resulted the most abundant sequence information and the longest sequences, but the assembly process took a long time; meanwhile, SOAPdenovo and IDBA-UD cost a relatively short time, but generated less sequence information and shorter sequences in the assembly results. Thus, it is recom-mended to use Trinity software to assemble virus genome based on transcriptome data.
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