.. _Trinity:

Trinity
=======

De acordo com o `página do Trinity <https://github.com/trinityrnaseq/trinityrnaseq/wiki>`_,
"*Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem,
represents a novel method for the efficient and robust de novo reconstruction of
transcriptomes from RNA-seq data. Trinity combines three independent software
modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process
large volumes of RNA-seq reads. Trinity partitions the sequence data into many
individual de Bruijn graphs, each representing the transcriptional complexity at
a given gene or locus, and then processes each graph independently to extract
full-length splicing isoforms and to tease apart transcripts derived from paralogous genes*".


Versões Disponíveis
-------------------

* trinity/2.8.5


Submissão de Jobs
-----------------

Crie um arquivo chamado, por exemplo, *submit_jobs.sh*.

.. code-block:: bash

   #!/bin/bash
   #SBATCH -t 23:00:00 -c 4
   
   #######################################################
   ##  Run Trinity to Generate Transcriptome Assemblies ##
   #######################################################
   
   module load trinity/2.8.5
   
   export INPUT="reads.left.fq.gz reads.right.fq.gz"
   export OUTPUT="trinity_OutDir_01"
   
   job-nanny Trinity --seqType fq --max_memory 2G \
             --left reads.left.fq.gz \
             --right reads.right.fq.gz \
             --SS_lib_type RF \
             --output trinity_OutDir_01 \
             --CPU 4

Para submeter o processo, basta usar o comando:

.. code-block:: bash

   sbatch submit_jobs.sh

Referências
-----------

Para informações adicionais sobre o software, consulte a `documentação do Trinity <https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity>`_.