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.

Más información

Página web de Trinity.