Documentation by Shelby Williams

Trinity is an assembler of RNA-seq reads, after they have been trimmed. Trinity uses three programs (Inchworm, Chrysalis, and Butterfly) to assemble large volumes of transcriptome reads. The output of Trinity is the Trinity.fasta file found in the /trinity_out_dir/ folder/

A simple Trinity shell script:

#!/bin/bash

#$ -S /bin/bash

. /etc/profile

#$ -cwd

#$ -pe threaded 10

export PATH=/opt/perun/jre1.8.0_121/bin:$PATH /opt/perun/trinityrnaseq-Trinity-v2.4.0/Trinity –seqType fq –left RetortaCarp_1_PairNtrim.fastq –right RetortaCarp_2_PairNtrim.fastq –CPU 10 –max_memory 20G

#Note: this is for Trinity version 2.4.0. You made need to update the path to other versions of Trinity as they become installed on perun.