Trinity

Overview

Trinity is a software for de novo transcriptome assembly, a process that reconstructs transcript sequences from RNA-Seq data without any reliance on a pre-exising genome.

Availability

Cluster	Module/Version
BOSE	trinityrnaseq/2.15.2
BGSC	Not Available

Arguments / Options

This is a list of arguments for the Trinity command that we wanted to highlight.

Option	Description
--help	Display the help file
--max_memory	Set to below your requested Slurm memory. Example: "10G"
--CPU	Number of CPUs to use - recommended to set to `$SLURM_NTASKS`
$TRINITY_HOME	Environment variable pointing to Trinity install, useful for accessing files in `util` directory

Utility Scripts

Trinity comes with several pre-built utility scripts that may be useful for your work, many of which are perl-based.

View Available Scripts

ls $TRINITY_HOME/util
ls $TRINITY_HOME/util/misc/

Running Example:

perl $TRINITY_HOME/util/misc/run_bowtie2.pl --target File.fasta --left left.fq --right right.fq

Other Tools

Trinity comes with several others programs built in, such as bowtie2, blastx, and samtools.

To access these tools, you'll need to prefix your command with TrinityExec as everything lives in a container.

For Example: TrinityExec "bowtie2 --help"

Sample Slurm Script

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load trinityrnaseq/2.15.2   # Load Trinity
Trinity --seqType fq --max_memory 15G --left file_1.fq  --right file_2.fq --CPU $SLURM_NTASKS

Real Example

Has your research group used Trinity in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation in your papers to support continued development of NBIA Data Retriever.

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883. PubMed PMID: 21572440.