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Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

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Rascaf: Improving Genome Assembly with RNA Sequencing Data.

Li Song, Dhruv S Shankar, Liliana Florea

The Plant Genome

|December 1, 2016

Summary

This summary is machine-generated.

Rascaf, a new bioinformatics tool, improves genome assembly by using intron spanning RNA sequencing (RNA-seq) data to connect DNA fragments. This enhances gene annotation accuracy and genome completeness.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Short sequencing reads from second-generation sequencing technologies result in fragmented genomes and incomplete gene annotations.
Existing bioinformatics methods struggle to fully leverage RNA sequencing data for improving genome assembly contiguity and completeness.

Purpose of the Study:

To develop a novel bioinformatics tool, Rascaf, for enhancing genome assembly using RNA sequencing data.
To improve the contiguity and completeness of draft genome assemblies and subsequent gene annotations.

Main Methods:

Rascaf utilizes long-range continuity information from intron spanning RNA sequencing (RNA-seq) read pairs.
It constructs an exon block graph representing gene structure and contig relationships.
A heaviest path algorithm is employed to identify new contig connections.

Main Results:

Rascaf successfully detects thousands of new, verifiable connections in draft Rosaceae genomes.
The tool demonstrates higher accuracy and precision compared to existing methods.
Incorporation of Rascaf into sequencing pipelines significantly improves genome assembly and gene annotation.

Conclusions:

Rascaf is an efficient and practical tool for improving genome assembly and gene annotation.
Leveraging RNA-seq data with Rascaf offers a robust solution to challenges posed by fragmented genomes.
The tool can be readily integrated into standard sequencing workflows to enhance genomic data quality.