SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
文献类型：期刊论文
| 作者 | Xie Yinlong; Wu Gengxiong; Tang Jingbo; Luo Ruibang; Patterson Jordan; Liu Shanlin; Huang Weihua; He Guangzhu; Gu Shengchang; Li Shengkang |
| 刊名 | BIOINFORMATICS
 |
| 出版日期 | 2014 |
| 英文摘要 | Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs of next- generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge. Results: Here, we present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse. Using as our benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy and faster execution. |
| 收录类别 | SCI |
| 原文出处 | http://bioinformatics.oxfordjournals.org/content/30/12/1660 |
| 语种 | 英语 |
| 源URL | [http://ir.siat.ac.cn:8080/handle/172644/6211]  |
| 专题 | 深圳先进技术研究院_其他 |
| 作者单位 | BIOINFORMATICS |
| 推荐引用方式 GB/T 7714 | Xie Yinlong,Wu Gengxiong,Tang Jingbo,et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads[J]. BIOINFORMATICS,2014. |
| APA | Xie Yinlong.,Wu Gengxiong.,Tang Jingbo.,Luo Ruibang.,Patterson Jordan.,...&Wang Jun.(2014).SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.BIOINFORMATICS. |
| MLA | Xie Yinlong,et al."SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads".BIOINFORMATICS (2014). |
入库方式： OAI收割
来源：深圳先进技术研究院
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