Bridger: a new framework for de novo transcriptome assembly using RNA-seq data

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0596-2) contains supplementary material, which is available to authorized users.

Mechanisms of vegetative propagation in bulbs : a molecular approach

“…Transcripts expressed at extremely low levels can also cause noise because they may not be reliably assembled (http://cole-trapnell-lab.github.io/cufflinks/cufflinks/). Furthermore, it is difficult to distinguish between isoforms of one gene versus the existence of more gene copies as a consequence of duplications (Chang et al 2015).…”

Transcriptome Analysis for Non-Model Organism: Current Status and Best-Practices

“…However, de Bruijn graph-based strategy between de novo genome and transcriptome assembly is slightly modiied because of the following reasons: (i) while the DNA sequencing depth is expected to be uniform across the genome (except in repetitive regions), the sequencing depth of transcripts can vary considerably, (ii) Genome assembly graph is considered as linear (theoretically one graph for each chromosome), but due to alternative splicing, transcriptome assembly is more complex than genome and requires a graph to represent the multiple alternative transcripts per locus [1,21]. By considering these challenges, several de novo assembly tools such as Trinity [1], SOAPdenovo-Trans [22], Trans-AbySS [23], Oases [24], IDBA-Tran [25], BinPacker [26] and Bridger [27] have been developed so far (Box 1). Most of these tools, which are initially developed for de novo genome assembly (except for Trinity) use de Bruijn graph-based assembly strategy and have their own pros and cons in transcript reconstruction.…”

Transcriptome assembly strategies for precision medicine

“…A method called Bridge which combines the de novo assembler Trinity with the reference-based assembler Cufflinks has been proposed [28] to tackle the transcriptome assembly problem. Bridge builds splicing graphs for all genes from the reference genome.…”