Trinity

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Description

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.

Availability

Verze 2012-06-8, 2013-11-10, 2014-04-13p1, 2.0.6 and 2.4.0. Available modules (from the oldest):

trinity
trinity-201311
trinity-201404
trinity-2.0.6
trinity-2.4.0

Use

module add trinity-2.4.0
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).

Documentation

https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running%20Trinity

Licence

See /software/trinity/LICENSE or https://github.com/trinityrnaseq/trinityrnaseq/blob/master/LICENSE

Program manager

meta@cesnet.cz

Homepage

https://github.com/trinityrnaseq/trinityrnaseq/wiki

Know how

To combine with R, apply module R-3.1.1.