Computational approaches for transcriptome assembly based on sequencing technologies: A survey

(E-pub Abstract Ahead of Print)

Author(s): Yuwen Luo, Xingyu Liao, Fang-Xiang Wu, Jianxin Wang*.

Journal Name: Current Bioinformatics

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Abstract:

Transcriptome assembly plays a critical role in studying biological properties and examining the expression levels of genomes in specific cells. It is also the basis of many downstream analyses. With the increase of sequencing speed and the decrease of sequencing cost, massive sequencing data continues to accumulate. A large number of assembly strategies based on different computational methods and experiments have been developed. How to efficiently perform transcriptome assembly with high sensitivity and accuracy becomes a key issue. In this work, these biological problems are explored based on different sequencing technologies. Specifically, transcriptome assembly with next-generation sequencing reads is divided into reference-based assembly and de novo assembly. The examples of different species are used to illustrate that long reads produced by third-generation sequencing can cover full-length transcripts without assembly. In addition, assembly also can be performed using the Hybrid-seq method. Besides, some tools for transcriptome assembly are summarized. Finally, we discuss the future directions of transcriptome assembly.

Keywords: Transcriptome assembly, sequencing technologies, Hybrid-Seq, full-length transcript, annotation

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Article Details

(E-pub Abstract Ahead of Print)
DOI: 10.2174/1574893614666190410155603
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