| Hilfe-Text | 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.
DOCUMENTATION
* TRINITY User Guide, Documents, Wiki-Article
https://github.com/trinityrnaseq/trinityrnaseq/wiki
Local HPC Documentations: /opt/bwhpc/common/bio/trinity/2.2.0/hpc_conf
Best-Practices-Repository: http://www.bwhpc-c5.de/wiki/index.php/Trinity
* TRINITY Download
https://github.com/trinityrnaseq/trinityrnaseq/wiki
* bwHPC examples and a moab example script can be found here:
/opt/bwhpc/common/bio/trinity/2.2.0/hpc_conf
/opt/bwhpc/common/bio/trinity/2.2.0/bwhpc-examples
* PLUGINS
JellyFish
Inchworm
Chrysalis
QuantifyGraph
GraphFromFasta
ReadsToTranscripts
fastool
parafly
samtools-0.1.19
CITATION
See section 'Referencing Trinity' here:
https://github.com/trinityrnaseq/trinityrnaseq/wiki
In case of problems, please contact: bwhpc (at) uni-konstanz.de
This module is available for all users. |