SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
University of Copenhagen · Central South University · +5 more institutions
Abstract
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…
Citation impact
- FWCI
- 42.82
- Percentile
- 100%
- References
- 19
Authors
16- YXYinlong XieCorresponding
University of Copenhagen, Central South University, Novo Nordisk Foundation, Chinese University of Hong Kong, Shenzhen, Shenzhen Institutes of Advanced Technology, University of Hong Kong, South China University of Technology
- GWGengxiong Wu
University of Copenhagen, Central South University, Novo Nordisk Foundation, Chinese University of Hong Kong, Shenzhen, Shenzhen Institutes of Advanced Technology, University of Hong Kong, South China University of Technology
- JTJingbo Tang
University of Copenhagen, Central South University, Novo Nordisk Foundation, Chinese University of Hong Kong, Shenzhen, Shenzhen Institutes of Advanced Technology, University of Hong Kong, South China University of Technology
- RLRuibang Luo
University of Copenhagen, Central South University, Novo Nordisk Foundation, Chinese University of Hong Kong, Shenzhen, Shenzhen Institutes of Advanced Technology, University of Hong Kong, South China University of Technology
- JPJordan Patterson
University of Copenhagen, Central South University, Novo Nordisk Foundation, Chinese University of Hong Kong, Shenzhen, Shenzhen Institutes of Advanced Technology, University of Hong Kong, South China University of Technology
Topics & keywords
- Transcriptome
- RNA-Seq
- De novo transcriptome assembly
- Sequence assembly
- Computational biology
- Genome
- Redundancy (engineering)
- Computer science