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noviembre, 2013:

Trinity

General information

2.1.1 release. Trinity, 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.

How to use

You can use the

send_trinity

command to submit jobs to the queue system. After answering few questions a script will be created and submitted to the queue system. For advanced users it can be used to generate a sample script.

Performance

Trinity can be run in parallel but it is not very efficient above 4 cores with low performance, as can be seen in the the table. Trinity consumes high amounts of RAM.

Performance of Trinity
Cores  1 4 8 12
Time 5189 2116 1754 1852
Speddup 1 2.45 2.96 2.80
Efficiency (%)  100 61 37 23

 

More information

Trinity web page.

Trinity

Información general

2.1.1 release. Trinity, 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.

Cómo usar

Se puede usar el comando:

send_trinity

para enviar trabajos al sistema de colas. Tras responder unas preguntas creará el script que se enviará al sistema de colas. Para usuarios avanzados se puede utilizar para generar un script de ejemplo.

Rendimiento

A pesar de que Trinity puede ejecutarse en paralelo no lo hace de forma eficiente por encima 4 cores, siendo la reducción del tiempo de computo muy pequeña al aumentar el número de cores de cálculo como se observa en la tabla. Trinity es un programa que consume grandes cantidades de RAM.

Rendimiento de Trinity
Cores  1 4 8 12
Tiempo 5189 2116 1754 1852
Aceleración 1 2.45 2.96 2.80
Eficiencia (%)  100 61 37 23

 

Más información

Página web de Trinity.

Trinity

Información general

2.1.1 release. Trinity, 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.

Nola erabili

send_trinity

komandoa erabili daiteke lanak koletara bidaltzeko. Galdera batzuk erantzun eta gero koletara bidali behar den scripta sortu eta bidaliko du. Erabiltzaile  aurreratuentzak erabili daiteke ere adibide scrtip bat sortzeko.

Errendimendua

Trinity paraleloan exekutatu daiteke baina errendimendu txarrarekin 4 koretik gora, nahiz eta kore kopurua asko igo kalkulu denbora ez da asko jaisten. Trinimyk RAM asko erabiltzen du.

Trinityren errendimendua
Koreak  1 4 8 12
Denbora 5189 2116 1754 1852
Azelerazioa 1 2.45 2.96 2.80
Eraginkortasuna (%)  100 61 37 23

 

Informazio gehiago

Página web de Trinity.