Trinity

De acordo com o página do Trinity, “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”.

Versões Disponíveis

• trinity/2.8.5

Submissão de Jobs

Crie um arquivo chamado, por exemplo, submit_jobs.sh.

#!/bin/bash
#SBATCH -t 23:00:00 -c 4

#######################################################
##  Run Trinity to Generate Transcriptome Assemblies ##
#######################################################

module load trinity/2.8.5

export INPUT="reads.left.fq.gz reads.right.fq.gz"
export OUTPUT="trinity_OutDir_01"

job-nanny Trinity --seqType fq --max_memory 2G \
          --left reads.left.fq.gz \
          --right reads.right.fq.gz \
          --SS_lib_type RF \
          --output trinity_OutDir_01 \
          --CPU 4

Para submeter o processo, basta usar o comando:

sbatch submit_jobs.sh

Referências

Para informações adicionais sobre o software, consulte a documentação do Trinity.