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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.

Installed version

The follofwing versions of Trinity are currently installed (sorted by environment):


  • Trinity/2.2.0
  • Trinity/2.4.0


  • Trinity/2.6.6-intel-2018a
  • Trinity/2.8.4-foss-2017b


  • Trinity/2.14.0-foss-2019b-Python-3.7.4

Using Trinity

To use Trinity, you just have to load the corresponding module. For the newest version, 2.6.6 that is, you have to change the environment first.

module load hpc-env/6.4
module load 2.6.6-intel-2018a


The full documentation can be found here.