Trinity
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.
License
See /software/trinity/LICENSE or https://github.com/trinityrnaseq/trinityrnaseq/blob/master/LICENSE
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of trinity and load default version of trinity as
module avail trinity/ # list available modules module load trinity # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail trinity
and choose explicit version you want to use. 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.
Documentation
https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running%20Trinity