Trinity as a Framework for De novo Transcriptome Assembly and Analysis

Transcriptome sequencing via RNA-Seq provides a powerful method for transcript discovery and gene expression analysis in both model and non-model organisms.   De novo transcriptome assembly, as performed by our Trinity software, enables transcript discovery and analysis for organisms where reference genome assemblies are lacking or are sufficiently different from the transcriptome under study.

Since the initial development of Trinity, we have concentrated effort on integrating tools to facilitate analysis efforts beyond transcript reconstruction, including analysis of differential expression, identification and functional annotation of likely protein-coding sequences, transcript-based polymorphism discovery, and fusion gene detection such as in cancer.

Here, we describe the composition of the Trinity software and provide examples of downstream applications, in the context of reference genomes and for genome-free studies, tackling research problems across diverse eukaryotes.