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Kategorie/Name/Versionbio/trinity/2.2.0
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LizenzGPL | see LICENSE.txt
URL https://github.com/trinityrnaseq
What-isbio/trinity/2.2.0 : Trinity 2.2.0 assembles transcript sequences from Illumina RNA-Seq data.
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.
SupportbwHPC Support-Portal
Installationsdatum05.10.2017
Löschdatum
Best-Practice-Wikihttp://www.bwhpc-c5.de/wiki/index.php/Trinity