Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data.

ABSTRACT:

Background

Rapid advances in next-generation sequencing methods have provided new opportunities for transcriptome sequencing (RNA-Seq). The unprecedented sequencing depth provided by RNA-Seq makes it a powerful and cost-efficient method for transcriptome study, and it has been widely used in model organisms and non-model organisms to identify and quantify RNA. For non-model organisms lacking well-defined genomes, de novo assembly is typically required for downstream RNA-Seq analyses, including SNP discovery and identification of genes differentially expressed by phenotypes. Although RNA-Seq has been successfully used to sequence many non-model organisms, the results of de novo assembly from short reads can still be improved by using recent bioinformatic developments.

Results

SUBMITTER: Duan J 

PROVIDER: S-EPMC3485621 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature