Bridger: a new framework for de novo transcriptome assembly using RNA-seq data.
We present a new de novo transcriptome assembler, Bridger, which takes advantage of techniques employed in Cufflinks to overcome limitations of the existing de novo assemblers. When tested on dog, human, and mouse RNA-seq data, Bridger assembled more full-length reference transcripts while reporting considerably fewer candidate transcripts, hence greatly reducing false positive transcripts in comparison with the state-of-the-art assemblers. It runs substantially faster and requires much less memory space than most assemblers. More interestingly, Bridger reaches a comparable level of sensitivity and accuracy with Cufflinks. Bridger is available at https://sourceforge.net/projects/rnaseqassembly/files/?source=navbar.
Zheng
Z
Chang
Guojun
G
Li
Juntao
J
Liu
Yu
Y
Zhang
Cody
C
Ashby
Deli
D
Liu
Carole L
CL
Cramer
Xiuzhen
X
Huang
D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D066264:Datasets as Topic; D004285:Dogs; D020869:Gene Expression Profiling / Q000379:methods; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020407:Internet; D051379:Mice; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome