Trinity r20131110

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 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.

Module file

The module file can be found in this location:

 /cm/shared/modulefiles/SHARED/

<source lang='tcl'>

1. %Module1.0#######################################################################
   1. Trinity r20131110 modulefile

proc ModulesHelp { } {

       puts stderr "\tAdds Trinity r20131110 to your environment"

}

module-whatis "Adds Trinity r20131110 to your environment"

module load bowtie/1-1.0.0

set trinity_r20131110_root /cm/shared/apps/SHARED/Trinity/trinityrnaseq_r20131110/

prepend-path PATH $trinity_r20131110_root

</source>

Installation details

The source was downloaded from SourceForge on 15-03-2014:

 http://sourceforge.net/projects/trinityrnaseq/files/

Building of Inchworm and Chrysalis was done by simply issuing: <source lang='bash'> make </source>

See also

• Globally installed software
• ABGC specific modules

External links

• Trinity home page
• Nature Biotechnology paper on Trinity