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

• DOI: 10.1186/s12864-018-4567-3
• Publication Date: 2018-03-02T07:07:15Z
• Authors: Bai-Han Zhu; Jun Xiao; Wei Xue; Gui-Cai Xu; Ming-Yuan Sun; Jiong-Tang Li
• Keywords: 0303 health sciences; Single-molecule sequencing; Genome, Human; Methodology Article; Genome scaffolding; RNA-sequencing; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA; QH426-470; 03 medical and health sciences; Genetics; Humans; RNA; circRNA; TP248.13-248.65; Algorithms; Software; Biotechnology

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