Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms, transcripts from recently duplicated genes and transcriptomes from Illumina RNA-seq data.

Trinity is available as a module on Apocrita.


To run the latest installed version of Trinity, simply load the trinity module:

module load trinity

For usage documentation, run Trinity -h.

Example jobs

Serial job

Here is an example job running on 2 cores and 10GB total memory:

#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=2:0:0
#$ -l h_vmem=5G

module load trinity
Trinity --seqType fq \
        --max_memory 10G \
        --left reads.left.fq.gz \
        --right reads.right.fq.gz \
        --CPU ${NSLOTS}