Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
复制标题
DOI：
10.1186/1471-2164-11-663
复制
发表时间：
2010-11-24
期刊：
影响因子：
4.4
通讯作者：
Wang Z
中科院分区：
文献类型：
--
作者：
Martin J;Bruno VM;Fang Z;Meng X;Blow M;Zhang T;Sherlock G;Snyder M;Wang Z
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. 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. These results demonstrate that the Rnnotator pipeline is able to reconstruct full-length transcripts in the absence of a complete reference genome.
登录
查看更多内容
影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
影响因子：
48
作者：
Pepke, Shirley;Wold, Barbara;Mortazavi, Ali
通讯作者：
Mortazavi, Ali
影响因子：
46.9
作者：
通讯作者：
--
影响因子：
3
作者：
通讯作者：
--
影响因子：
48
作者：
Mortazavi, Ali;Williams, Brian A.;Wold, Barbara
通讯作者：
Wold, Barbara