IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing.
IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing.
复制标题
DOI：
10.1093/bioinformatics/bty098
复制
发表时间：
2018-07-01
期刊：
影响因子：
--
通讯作者：
Au KF
中科院分区：
文献类型：
--
作者：
Fu S;Ma Y;Yao H;Xu Z;Chen S;Song J;Au KF
在过去的几年中，长读段（LR）测序技术，如太平洋生物科学公司和牛津纳米孔技术公司，已被证明大大提高了基因组组装和转录组表征的质量。与通过LR测序进行基因组组装的高成本相比，生成用于转录组表征的LR更经济实惠。也就是说，当信息性转录组LR数据在没有高质量基因组的情况下可用时，高度需要用于从头转录组组装和注释的方法。在没有参考基因组的情况下，IDP-denovo通过整合LR和短读段的优势来进行从头转录组组装、同种型注释和定量。使用GM 12878人类数据作为金标准，我们证明了IDP-denovo具有上级转录本组装灵敏度和高准确度的异构体注释。此外，IDP-denovo输出两个丰度指数，以提供基因/亚型的全面表达谱。IDP-denovo代表了用于非模式生物研究的转录组组装、亚型注释和定量的稳健方法。将IDP-denovo应用于非模式生物铁皮石斛（Dendrobium officinale），我们发现了一些现有注释文库未报道的新基因和新亚型。这些结果揭示了铁皮石斛基因异构体的高度多样性，这在现有的注释文库中是没有报道的。本研究中使用/分析的铁皮石斛数据集已保存在SRA中，登录号为SRP 094520。IDP-denovo可从www.healthcare.uiowa.edu/labs/au/IDP-denovo/下载。 补充数据可在Bioinformatics在线获得。
In the past years, the long read (LR) sequencing technologies, such as Pacific Biosciences and Oxford Nanopore Technologies, have been demonstrated to substantially improve the quality of genome assembly and transcriptome characterization. Compared to the high cost of genome assembly by LR sequencing, it is more affordable to generate LRs for transcriptome characterization. That is, when informative transcriptome LR data are available without a high-quality genome, a method for de novo transcriptome assembly and annotation is of high demand. Without a reference genome, IDP-denovo performs de novo transcriptome assembly, isoform annotation and quantification by integrating the strengths of LRs and short reads. Using the GM12878 human data as a gold standard, we demonstrated that IDP-denovo had superior sensitivity of transcript assembly and high accuracy of isoform annotation. In addition, IDP-denovo outputs two abundance indices to provide a comprehensive expression profile of genes/isoforms. IDP-denovo represents a robust approach for transcriptome assembly, isoform annotation and quantification for non-model organism studies. Applying IDP-denovo to a non-model organism, Dendrobium officinale, we discovered a number of novel genes and novel isoforms that were not reported by the existing annotation library. These results reveal the high diversity of gene isoforms in D.officinale, which was not reported in the existing annotation library. The dataset of Dendrobium officinale used/analyzed during the current study has been deposited in SRA, with accession code SRP094520. IDP-denovo is available for download at www.healthcare.uiowa.edu/labs/au/IDP-denovo/. Supplementary data are available at Bioinformatics online.
登录
查看更多内容
影响因子：
12.3
作者：
Gonzàlez-Porta M;Frankish A;Rung J;Harrow J;Brazma A
通讯作者：
Brazma A
IDP-ASE：通过混合测序在基因和基因亚型水平上对等位基因特异性表达进行单倍型分析和定量
影响因子：
14.9
作者：
Deonovic B;Wang Y;Weirather J;Wang XJ;Au KF
通讯作者：
Au KF
DOI：
10.1073/pnas.1507125112
发表时间：
2015-06-09
影响因子：
11.1
作者：
Darmanis S;Sloan SA;Zhang Y;Enge M;Caneda C;Shuer LM;Hayden Gephart MG;Barres BA;Quake SR
通讯作者：
Quake SR
影响因子：
9.1
作者：
Chen Geng;Yin KangPing;Shi TieLiu
通讯作者：
Shi TieLiu
影响因子：
5.8
作者：
Li, WZ;Jaroszewski, L;Godzik, A
通讯作者：
Godzik, A