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#!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
CPU=$(nproc || sysctl -n hw.physicalcpu)
## use jellyfish
../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU ${CPU} --normalize_reads --no_cleanup --output trinity_test_no_qtrim
##### Done Running Trinity #####
if [ ! $* ]; then
exit 0
fi
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