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====== Trinity - Assembly of transcriptome reads ======
Documentation by Shelby Williams

Trinity is an assembler of RNA-seq reads, after they have been trimmed. Trinity uses three programs (Inchworm, Chrysalis, and Butterfly) to assemble large volumes of transcriptome reads. The output of Trinity is the Trinity.fasta file found in the /trinity_out_dir/ folder/

----


A simple Trinity shell script, using the new conda-environments:
<code>
#!/bin/bash
#$ -S /bin/bash
. /etc/profile
#$ -cwd
#$ -pe threaded 10

source activate trinity
Trinity --seqType fq --left RetortaCarp_1_PairNtrim.fastq --right RetortaCarp_2_PairNtrim.fastq --CPU 10 --max_memory 20G
source deactivate
</code>
#Note: this should always invoke the latest version of Trinity installed on perun. You can check this by looking at the output file or invoking Trinity directly from the prompt with Trinity --version. 

**ATTENTION!**

Trinity 2.4.0 is not compatible with Bowtie2. Skip this step by adding the flag **--no_bowtie**