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Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, 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 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. Briefly, the process works like so:

  • Inchworm assembles the RNA-seq data into the unique sequences of transcripts, often generating full-length transcripts for a dominant isoform, but then reports just the unique portions of alternatively spliced transcripts.
  • Chrysalis clusters the Inchworm contigs into clusters and constructs complete de Bruijn graphs for each cluster. Each cluster represents the full transcriptonal complexity for a given gene (or sets of genes that share sequences in common). Chrysalis then partitions the full read set among these disjoint graphs.
  • Butterfly then processes the individual graphs in parallel, tracing the paths that reads and pairs of reads take within the graph, ultimately reporting full-length transcripts for alternatively spliced isoforms, and teasing apart transcripts that corresponds to paralogous genes.


See /software/trinity/LICENSE or


module avail trinity/ # list available modules
module load trinity   # load (default) module

Then run as

Trinity --version
Trinity --help
Trinity --CPU 20

for run on 20 processors. For details see Documentaion.

Perl libriraries, plugins etc. are saved in /software/trinity or /software/trinity/VERSION.

Trinity-2.0.6 requires jdk-7 (not work with jdk-8), therefore be careful with adding other modules (ideally, add trinity module as the last one).

Trinity-2.9.1 employs module openjdk-10, not jdk-*

With R

To combine with R, apply module R-3.1.1.