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#!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
if [ -z ${TRINITY_HOME} ]; then
echo "Must set env var TRINITY_HOME"
exit 1
fi
CPU=$(nproc || sysctl -n hw.physicalcpu)
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
--left reads.left.fq.gz \
--right reads.right.fq.gz \
--SS_lib_type RF \
--CPU ${CPU} \
--output trinity_out_dir_noseqtk --NO_SEQTK
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