.. _backbone-label:

Trinity
==============================

Introduction
~~~~~~~~
Trinity assembles transcript sequences from Illumina RNA-Seq data.


| For more information, please check:
| BioContainers: https://biocontainers.pro/tools/trinity 
| Home page: https://github.com/trinityrnaseq/trinityrnaseq/

.. note::
    Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions
~~~~~~~
.. list-table::
  :width: 100 %
  :widths: 25 75
  :header-rows: 1

  * - Cluster
    - Version(s)

  * - ANVIL
    - 2.12.0, 2.13.2, 2.14.0, 2.15.0
  * - BELL
    - 2.12.0, 2.13.2, 2.14.0, 2.15.0
  * - GAUTSCHI
    - 2.12.0, 2.13.2, 2.14.0, 2.15.0
  * - NEGISHI
    - 2.12.0, 2.13.2, 2.14.0, 2.15.0
  * - SCHOLAR
    - 2.12.0, 2.13.2, 2.14.0, 2.15.0

Commands
~~~~~~~
- Trinity
- TrinityStats.pl
- Trinity_gene_splice_modeler.py
- ace2sam
- align_and_estimate_abundance.pl
- analyze_blastPlus_topHit_coverage.pl
- analyze_diff_expr.pl
- blast2sam.pl
- bowtie
- bowtie2
- bowtie2-build
- bowtie2-inspect
- bowtie2sam.pl
- contig_ExN50_statistic.pl
- define_clusters_by_cutting_tree.pl
- export2sam.pl
- extract_supertranscript_from_reference.py
- filter_low_expr_transcripts.pl
- get_Trinity_gene_to_trans_map.pl
- insilico_read_normalization.pl
- interpolate_sam.pl
- jellyfish
- novo2sam.pl
- retrieve_sequences_from_fasta.pl
- run_DE_analysis.pl
- sam2vcf.pl
- samtools
- samtools.pl
- seq_cache_populate.pl
- seqtk-trinity
- sift_bam_max_cov.pl
- soap2sam.pl
- tabix
- trimmomatic
- wgsim
- wgsim_eval.pl
- zoom2sam.pl

Module
~~~~~~~~
You can load the modules by::

    module load biocontainers
    module load trinity

Example job
~~~~~
.. warning::
    Using ``#!/bin/sh -l`` as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use ``#!/bin/bash`` instead.

To run trinity on our clusters:

.. tab-set::

  .. tab-item:: Anvil

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A myallocation     # Allocation name
        #SBATCH -p wholenode        # Partition name
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=trinity
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers trinity

        # Your trinity workflow...

  .. tab-item:: Bell, Gautschi, or Negishi

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p cpu         # Partition name
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=trinity
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers trinity

        # Your trinity workflow...

  .. tab-item:: Gautschi-AI

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p ai          # Partition name
        #SBATCH --gres=gpu:1   # Number of GPUs
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=trinity
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers trinity

        # Your trinity workflow...

  .. tab-item:: Gilbreth

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p a100        # Partition name
        #SBATCH --gres=gpu:1   # Number of GPUs
        #SBATCH --mem=2G       # Memory
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=trinity
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers trinity

        # Your trinity workflow...

  .. tab-item:: Scholar

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A queue     # Queue name
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=trinity
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers trinity

        # Your trinity workflow...