Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, 2800 Mitchell Drive, MS100 Walnut Creek, California 94598, USA.
Nat Rev Genet. 2011 Sep 7;12(10):671-82. doi: 10.1038/nrg3068.
Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalogue of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies - along with some perspectives on transcriptome assembly in the near future.
转录组学研究通常依赖于部分参考转录组，这些转录组无法捕获完整的转录本目录及其变体。测序技术和组装算法的最新进展使得即使没有参考基因组，也可以通过深度 RNA 测序（RNA-seq）来重建整个转录组。然而，从数十亿条通常非常短的 RNA-seq 读取中进行转录组组装带来了重大的信息学挑战。本文综述了转录组组装方法的最新进展——基于参考、从头和组合策略——以及对未来转录组组装的一些展望。
