P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

文献类型： 外文期刊

第一作者： Zhu, Bai-Han

作者： Zhu, Bai-Han;Xiao, Jun;Xue, Wei;Xu, Gui-Cai;Sun, Ming-Yuan;Li, Jiong-Tang;Zhu, Bai-Han;Xiao, Jun;Xue, Wei;Xu, Gui-Cai;Sun, Ming-Yuan;Li, Jiong-Tang;Zhu, Bai-Han;Xiao, Jun;Sun, Ming-Yuan;Xu, Gui-Cai

作者机构：

关键词： RNA-sequencing; Genome scaffolding; Single-molecule sequencing; circRNA

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2018 年 19 卷

页码：

收录情况： SCI

摘要： Background: Obtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene regions. Genomes are widely transcribed, generating messenger and non-coding RNAs. These widespread transcripts can be used to scaffold genomes and complete transcribed regions. Results: We present P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs. Tested in various species, P_RNA_scaffolder exhibited higher speed and efficiency than the existing state-of-the-art scaffolders. This tool also improved the contiguity of genome assemblies generated by current mate-pair scaffolding and third-generation single-molecule sequencing assembly. Conclusions: The P_RNA_scaffolder can improve the contiguity of genome assembly and benefit gene prediction.

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