Trinity

Trinity assembles transcript sequences from Illumina RNA-Seq data.

• Latest Version: v2.11.0
• Added: March, 2015
• Updated: October, 2020
• Link: https://trinityrnaseq.github.io

See versions of trinity which are available:

$ module avail trinity

Load one version into your environment and run it:

$ module load trinity/v2.11.0
$ Trinity

Notes about running Trinity:

• Please use the −−full_cleanup option so that Trinity can clean up after itself by removing all the intermediary files it has created except for the final fasta results
• Trinity creates millions of small files, which is inefficient and causes problems on the HPC storage server, so you please direct the output from these jobs to a directory inside /var/scratch instead of your home folder.
• For example:

• #!/usr/bin/env bash
  #SBATCH -p highmem
  #SBATCH -J trinity
  #SBATCH -n 8
  
  module load trinity/v2.6.6
  
  # create and change to a working directory on the compute node
  export WORKDIR=/var/scratch/$USER/$SLURM_JOBID
  mkdir -p $WORKDIR
  cd $WORKDIR
  
  # match CPUs to amount requested in SBATCH options!
  Trinity --seqType fq --max_memory 10G --left fish_R1.fastq --right fish_R2.fastq --CPU 8 --output trinity-fish2 --full_cleanup

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v2.11.0/trinityrnaseq-v2.11.0.FULL.tar.gz
$ tar xf trinityrnaseq-v2.11.0.FULL.tar.gz
$ cd trinityrnaseq-v2.11.0
$ sed -i 's/cmake/cmake3/' Chrysalis/Makefile Inchworm/Makefile
$ make
$ make plugins
$ sudo yum install python36-numpy.x86_64
$ sudo mkdir -p /export/apps/trinity/v2.11.0
$ sudo cp -r . /export/apps/trinity/v2.11.0
$ export TRINITY_HOME=/export/apps/trinity/v2.11.0
$ module load samtools/1.9 salmon/1.3.0 bowtie2/2.3.4.1 jellyfish/2.3.0
$ cd sample_data/test_Trinity_Assembly
$ ./runMe.sh

Consult the installing Trinity guide in the documentation.