Difference between revisions of "Trinity"
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== Introduction == | == Introduction == | ||
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: | 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. | *'''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. | ||
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== Installed version == | == Installed version == | ||
The currently installed version is | The follofwing versions of Trinity are currently installed (sorted by environment): | ||
'''hpc-uniol-env''' | |||
*'''Trinity/2.2.0''' | |||
*'''Trinity/2.4.0''' | |||
'''hpc-env/6.4''' | |||
*'''Trinity/2.6.6'''-intel-2018a | |||
*'''Trinity/2.8.4'''-foss-2017b | |||
'''hpc-env/8.3''' | |||
*'''Trinity/2.14.0'''-foss-2019b-Python-3.7.4 | |||
== Using Trinity == | |||
To use Trinity, you just have to load the corresponding module. | |||
For the newest version, 2.6.6 that is, you have to change the environment first. | |||
module load hpc-env/6.4 | |||
module load 2.6.6-intel-2018a | |||
== Documentation == | == Documentation == | ||
The full documentation can be found [https://github.com/trinityrnaseq/trinityrnaseq/wiki here]. | The full documentation can be found [https://github.com/trinityrnaseq/trinityrnaseq/wiki here]. | ||
Latest revision as of 11:48, 13 May 2022
Introduction
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.
Installed version
The follofwing versions of Trinity are currently installed (sorted by environment):
hpc-uniol-env
- Trinity/2.2.0
- Trinity/2.4.0
hpc-env/6.4
- Trinity/2.6.6-intel-2018a
- Trinity/2.8.4-foss-2017b
hpc-env/8.3
- Trinity/2.14.0-foss-2019b-Python-3.7.4
Using Trinity
To use Trinity, you just have to load the corresponding module. For the newest version, 2.6.6 that is, you have to change the environment first.
module load hpc-env/6.4 module load 2.6.6-intel-2018a
Documentation
The full documentation can be found here.
