Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach.
Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach.
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DOI：
10.1371/journal.pone.0031410
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Feulner PG
中科院分区：
文献类型：
--
作者：
Mundry M;Bornberg-Bauer E;Sammeth M;Feulner PG
对于非模式生物，转录组数据的数量正在迅速增加。随着测序技术的进步，重点转向解决生物信息学挑战，其中序列读取组装是第一个任务。最近的研究比较了不同软件的性能，以建立转录组组装的最佳实践。在这里，我们采用模拟的方法来评估汇编程序在454个数据上的具体特征。我们研究的新奇之处在于，模拟允许我们计算模型组件作为比较的参考点。通过模拟方法，我们可以将不同软件应用程序(CAP3、MIRA、Newbler和OASS)计算的组件的基本指标与已知的最佳解决方案进行比较。我们发现Mira和CAP3在合并读取方面是保守的。这导致了相对较高数量的短重叠群。相比之下，Newbler更容易将阅读片段合并成更长的重叠群，而绿洲则产生了总体最短的组装。由于模拟方法，阅读可以追溯到它们在转录组中的正确位置。再加上将读数映射到组装的重叠群上，我们能够评估组装中的歧义。这一分析进一步支持了MIRA和CAP3的保守性，这导致嵌合重叠群比例较低，但冗余度较高。Newbler产生的冗余较少，但嵌合重叠群的比例较高。我们对四个汇编程序的评估表明，Mira和Newbler的表现略高于其他程序，同时显示出截然不同的特点。在454次阅读中，OASS的表现不是很好。我们的评估表明，该软件在将读数合并为重叠群方面要么保守(Mira)，要么自由(Newbler)。这表明，在选择组装程序时，研究人员应该仔细考虑他们对所选方法的后续分析和结果，以获得组装。
The quantity of transcriptome data is rapidly increasing for non-model organisms. As sequencing technology advances, focus shifts towards solving bioinformatic challenges, of which sequence read assembly is the first task. Recent studies have compared the performance of different software to establish a best practice for transcriptome assembly. Here, we adapted a simulation approach to evaluate specific features of assembly programs on 454 data. The novelty of our study is that the simulation allows us to calculate a model assembly as reference point for comparison. The simulation approach allows us to compare basic metrics of assemblies computed by different software applications (CAP3, MIRA, Newbler, and Oases) to a known optimal solution. We found MIRA and CAP3 are conservative in merging reads. This resulted in comparably high number of short contigs. In contrast, Newbler more readily merged reads into longer contigs, while Oases produced the overall shortest assembly. Due to the simulation approach, reads could be traced back to their correct placement within the transcriptome. Together with mapping reads onto the assembled contigs, we were able to evaluate ambiguity in the assemblies. This analysis further supported the conservative nature of MIRA and CAP3, which resulted in low proportions of chimeric contigs, but high redundancy. Newbler produced less redundancy, but the proportion of chimeric contigs was higher. Our evaluation of four assemblers suggested that MIRA and Newbler slightly outperformed the other programs, while showing contrasting characteristics. Oases did not perform very well on the 454 reads. Our evaluation indicated that the software was either conservative (MIRA) or liberal (Newbler) about merging reads into contigs. This suggested that in choosing an assembly program researchers should carefully consider their follow up analysis and consequences of the chosen approach to gain an assembly.
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3.7
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通讯作者：
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