SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads
| Autor: | Xie, Yinlong, Wu, Gengxiong, Tang, Jingbo, Luo, Ruibang, Patterson, Jordan, Liu, Shanlin, Huang, Weihua, He, Guangzhu, Gu, Shengchang, Li, Shengkang, Zhou, Xin, Lam, Tak-Wah, Li, Yingrui, Xu, Xun, Wong, Gane Ka-Shu, Wang, Jun |
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| Rok vydání: | 2013 |
| Předmět: | |
| Druh dokumentu: | Working Paper |
| Popis: | Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining the sequences for a large number of genes from an organism with no reference genome. With the rapidly increasing throughputs and decreasing costs of next generation sequencing, RNA-Seq has gained in popularity; but given the typically short reads (e.g. 2 x 90 bp paired ends) of this technol- ogy, de novo assembly to recover complete or full-length transcript sequences remains an algorithmic challenge. Results: We present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. Its performance was evaluated on transcriptome datasets from rice and mouse. Using the known transcripts from these well-annotated genomes (sequenced a decade ago) as our benchmark, we assessed how SOAPdenovo- Trans and two other popular software handle the practical issues of alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy, and faster execution. Availability and Implementation: Source code and user manual are at http://sourceforge.net/projects/soapdenovotrans/ Contact: xieyl@genomics.cn or bgi-soap@googlegroups.com Comment: 7 pages, 4 figures, 3 tables |
| Databáze: | arXiv |
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