rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
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DOI：
10.1093/gigascience/giz100
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发表时间：
2019-09-01
期刊：
影响因子：
9.2
通讯作者：
Prjibelski, Andrey D.
中科院分区：
文献类型：
--
作者：
Bushmanova, Elena;Antipov, Dmitry;Prjibelski, Andrey D.
背景资料：产生大的RNA测序数据集的可能性已经导致了各种基于参考的和从头转录组组装器的发展，它们具有自己的优势和局限性。虽然基于参考的工具被广泛用于各种转录组学研究，但它们的应用仅限于具有完整和注释良好的基因组的生物体。从短读段的从头转录组重建仍然是一个开放的挑战性问题，这是复杂的不同基因，选择性剪接，和旁系同源基因的表达水平的变化。结果如下：在这里，我们描述了新的转录组组装rnaSPAdes，它已开发的SPAdes基因组组装程序的顶部，并探讨了计算之间的平行组装的转录组和单细胞基因组。我们还提出了rnaSPAdes组装的质量评估报告，将其与现代转录组组装工具进行比较，使用多种评估方法对各种RNA测序数据集进行评估，并简要强调不同组装器的优缺点。结论：基于不同组装方法之间的比较，我们推断不可能根据所有质量度量和所有使用的数据集来检测绝对领导者。然而，rnaSPAdes通常优于其他组装器的重要属性，如组装的基因和异构体的数量，同时与最接近的竞争对手相比，平均具有更高的准确性统计。
Background: The possibility of generating large RNA-sequencing datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the organisms with finished and well-annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing, and paralogous genes. Results: Herein we describe the novel transcriptome assembler rnaSPAdes, which has been developed on top of the SPAdes genome assembler and explores computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-sequencing datasets, and briefly highlight strong and weak points of different assemblers. Conclusions: Based on the performed comparison between different assembly methods, we infer that it is not possible to detect the absolute leader according to all quality metrics and all used datasets. However, rnaSPAdes typically outperforms other assemblers by such important property as the number of assembled genes and isoforms, and at the same time has higher accuracy statistics on average comparing to the closest competitors.