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

ABSTRACT:

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 co

SUBMITTER: Zhu BH 

PROVIDER: S-EPMC5834899 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature