SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
| Autor: | Shengchang Gu, Gengxiong Wu, Weihua Huang, Jordan Patterson, Gane Ka-Shu Wong, Ruibang Luo, Yingrui Li, Shengkang Li, Xun Xu, Yinlong Xie, Shanlin Liu, Jingbo Tang, Tak-Wah Lam, Xin Zhou, Jun Wang, Guangzhu He |
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| Rok vydání: | 2014 |
| Předmět: |
Statistics and Probability
De novo transcriptome assembly Sequence assembly RNA-Seq Computational biology Biology Biochemistry Genome DNA sequencing Transcriptome Mice Animals Molecular Biology Gene Genetics Sequence Analysis RNA Gene Expression Profiling Alternative splicing High-Throughput Nucleotide Sequencing Oryza Genomics Computer Science Applications Computational Mathematics Alternative Splicing Computational Theory and Mathematics Algorithms |
| Zdroj: | Bioinformatics (Oxford, England). 30(12) |
| ISSN: | 1367-4811 |
| Popis: | 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. Availability and implementation: Source code and user manual are available at http://sourceforge.net/projects/soapdenovotrans/. Contact: xieyl@genomics.cn or bgi-soap@googlegroups.com Supplementary information: Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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