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#!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
CPU=$(nproc || sysctl -n hw.physicalcpu)
# stop before inchworm (just in silico norm)
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} --output trinity_piecemeal --no_run_inchworm
# stop before chrysalis
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} --output trinity_piecemeal --no_run_chrysalis
# stop before phase 2
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} --output trinity_piecemeal --no_distributed_trinity_exec
# finish it up
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} --output trinity_piecemeal
##### Done Running Trinity #####
exit 0
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