Rnnotator: An automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

140Citations
Citations of this article
402Readers
Mendeley users who have this article in their library.

Abstract

ABSTRACT: BACKGROUND: Comprehensive annotation and quantification of transcriptomes are outstanding problems in functional genomics. While high throughput mRNA sequencing (RNA-Seq) has emerged as a powerful tool for addressing these problems, its success is dependent upon the availability and quality of reference genome sequences, thus limiting the organisms to which it can be applied. RESULTS: Here, we describe Rnnotator, an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome. We have applied the Rnnotator assembly pipeline to two yeast transcriptomes and compared the results to the reference gene catalogs of these organisms. The contigs produced by Rnnotator are highly accurate (95%) and reconstruct full-length genes for the majority of the existing gene models (54.3%). Furthermore, our analyses revealed many novel transcribed regions that are absent from well annotated genomes, suggesting Rnnotator serves as a complementary approach to analysis based on a reference genome for comprehensive transcriptomics. CONCLUSIONS: These results demonstrate that the Rnnotator pipeline is able to reconstruct full-length transcripts in the absence of a complete reference genome.

Cite

CITATION STYLE

APA

Martin, J., Bruno, V. M., Fang, Z., Meng, X., Blow, M., Zhang, T., … Wang, Z. (2010). Rnnotator: An automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics, 11(1). https://doi.org/10.1186/1471-2164-11-663

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free