Paper Info
Title
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 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 x 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.
Year
DOI
Venue
2014
10.1093/bioinformatics/btu077
BIOINFORMATICS
Field
DocType
Volume
Genome,De novo transcriptome assembly,RNA-Seq,Computer science,Transcriptome,Alternative splicing,DNA sequencing,Bioinformatics,Sequence assembly,Reference genome
Journal
30
Issue
ISSN
Citations 
12
1367-4803
11
PageRank 
References 
Authors
0.63
1
16
Name
Order
Citations
PageRank
Yinlong Xie1231.67
Gengxiong Wu2110.63
Jingbo Tang3110.63
Ruibang Luo41139.92
Jordan Patterson5110.63
Shanlin Liu6110.63
Weihua Huang7110.63
Guangzhu He8110.63
Shengchang Gu9110.63
Shengkang Li10110.97
Xin Zhou11141.42
Tak-Wah Lam121860164.96
Yingrui Li1355472.28
Xun Xu14152.36
Gane Ka-Shu Wong1516217.81
Jun Wang169228736.82