Tools for building de novo transcriptome assembly
Tools for building de novo transcriptome assembly
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DOI：
10.1016/j.cpb.2017.12.004
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发表时间：
2017-09-01
影响因子：
5.4
通讯作者：
Jaiswal, Pankaj
中科院分区：
文献类型：
--
作者：
Geniza, Matthew;Jaiswal, Pankaj
RNA-Seq 方法的可用性使研究人员能够从各种类型的生物样本中捕获转录组的空间或时间特征。除了差异基因表达分析之外，还可以在其测序的基因组或密切相关的基因组的背景下分析来自物种的转录组数据，以对生物样本特异性转录亚型、新的转录区域进行评分，并完善基因模型，包括新基因的识别。然而，许多重要的植物物种目前缺乏测序的基因组或密切相关的参考基因组，因此依赖从头方法来生成转录模型和转录组组装。在这里，我们描述了用于从头转录组组装的各种工具，并讨论了数据管理实践和标准。
The availability of RNA-Seq method allows researchers to capture the spatial or temporal profile of transcriptomes from various types of biological samples. The transcriptome data from a species can be analyzed in the context of its sequenced genomes or closely related genome to score biological sample-specific transcript isoforms, novel transcribed regions and to refine gene models including identification of new genes, in addition to the differential gene expression analysis. However, many plant species of importance currently lack a sequenced genome or a closely related reference genome and thus, rely on the de novo methods for generating transcript models and transcriptome assemblies. Here we describe various tools used for de novo transcriptome assembly and discuss the data management practices and standards.