SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads
Abstract
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: [email protected] or [email protected]
Keywords
Cite
@article{arxiv.1305.6760,
title = {SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads},
author = {Yinlong Xie and Gengxiong Wu and Jingbo Tang and Ruibang Luo and Jordan Patterson and Shanlin Liu and Weihua Huang and Guangzhu He and Shengchang Gu and Shengkang Li and Xin Zhou and Tak-Wah Lam and Yingrui Li and Xun Xu and Gane Ka-Shu Wong and Jun Wang},
journal= {arXiv preprint arXiv:1305.6760},
year = {2013}
}
Comments
7 pages, 4 figures, 3 tables