Trinity, developed at the Broad Institute, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.
Sample scripts for Trinity use are available in directory /opt/packages/examples/trinity on Bridges.
- The Trinity web site for information on Trinity command line options
- FAQ for Trinity on blacklight
- User-developed instructions for for building your own copy of Trinity
To see what versions of Trinity are available type
module avail trinity
To see what other modules are needed, what commands are available and how to get additional help type
module help trinity
To use Trinity, include a command like this in your batch script or interactive session to load the Trinity module:
module load trinity
Be sure you also load any other modules needed, as listed by the
module help trinity command.