Trinity assembles transcript sequences from Illumina RNA-Seq data.

• Latest Version: v2.4.0
• Added: March, 2015
• Updated: August, 2017
• Link: https://trinityrnaseq.github.io

See versions of trinity which are available:

$ module avail trinity

Note:

• You should 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 Trinity.fasta results file.
• Trinity creates millions of small files – which causes problems on the HPC storage server – so you must direct output from these jobs to /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/v2.4.0
  
  # 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/archive/Trinity-v2.4.0.zip
$ unzip Trinity-v2.4.0.zip
$ cd trinityrnaseq-Trinity-v2.4.0
$ scl enable devtoolset-4 bash
$ make
$ make plugins
$ sudo mkdir /export/apps/trinity/v2.4.0
$ make test_trinity
$ sudo cp -r . /export/apps/trinity/v2.4.0