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3-1.assembling_50_plastomes_using_NOVOPlasty.sh
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3-1.assembling_50_plastomes_using_NOVOPlasty.sh
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# get RUN_PATH
RUN_PATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
cd NOVOPlasty-plastome
# kmer=23
cd K23
cd ERR1917165-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR1917165.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602594-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602594.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602595-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602595.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602608-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602608.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602609-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602609.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602583-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602583.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602582-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602582.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602602-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602602.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602603-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602603.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd ERR964904-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR964904.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602589-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602589.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602588-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602588.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR6478596-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR6478596.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602584-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602584.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602585-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602585.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602605-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602605.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602604-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602604.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR4428742-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR4428742.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602576-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602576.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602577-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602577.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602593-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602593.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602592-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602592.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR2057084-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR2057084.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602599-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602599.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602598-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602598.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd ERR268390-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR268390.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR6932851-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR6932851.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602601-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602601.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602600-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602600.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602581-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602581.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602578-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602578.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602579-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602579.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5028199-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5028199.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602572-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602572.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602573-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602573.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602597-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602597.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602596-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602596.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602610-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602610.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR1145775-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR1145775.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd ERR2206741-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR2206741.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602575-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602575.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602574-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602574.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602590-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602590.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602591-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602591.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602606-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602606.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602607-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602607.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602587-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602587.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR5602586-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602586.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR2037123-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR2037123.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K23
cd SRR7630500-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR7630500.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/
# kmer=31
cd K31
cd ERR1917165-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR1917165.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602594-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602594.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602595-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602595.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602608-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602608.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602609-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602609.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602583-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602583.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602582-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602582.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602602-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602602.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602603-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602603.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd ERR964904-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR964904.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602589-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602589.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602588-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602588.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR6478596-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR6478596.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602584-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602584.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602585-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602585.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602605-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602605.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602604-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602604.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR4428742-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR4428742.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602576-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602576.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602577-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602577.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602593-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602593.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602592-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602592.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR2057084-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR2057084.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602599-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602599.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602598-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602598.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd ERR268390-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR268390.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR6932851-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR6932851.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602601-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602601.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602600-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602600.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602581-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602581.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602578-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602578.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602579-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602579.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5028199-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5028199.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602572-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602572.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602573-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602573.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602597-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602597.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602596-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602596.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602610-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602610.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR1145775-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR1145775.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd ERR2206741-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR2206741.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602575-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602575.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602574-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602574.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602590-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602590.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602591-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602591.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602606-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602606.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602607-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602607.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602587-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602587.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR5602586-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602586.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR2037123-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR2037123.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K31
cd SRR7630500-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR7630500.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/
# kmer=39
cd K39
cd ERR1917165-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR1917165.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602594-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602594.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602595-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602595.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602608-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602608.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602609-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602609.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602583-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602583.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602582-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602582.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602602-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602602.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602603-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602603.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd ERR964904-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR964904.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602589-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602589.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602588-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602588.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR6478596-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR6478596.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602584-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602584.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602585-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602585.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602605-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602605.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602604-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602604.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR4428742-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR4428742.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602576-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602576.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602577-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602577.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602593-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602593.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602592-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602592.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR2057084-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR2057084.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602599-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602599.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602598-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602598.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd ERR268390-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR268390.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR6932851-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR6932851.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602601-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602601.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602600-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602600.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602581-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602581.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602578-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602578.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602579-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602579.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5028199-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5028199.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602572-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602572.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602573-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602573.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602597-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602597.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602596-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602596.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602610-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602610.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR1145775-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR1145775.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd ERR2206741-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR2206741.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602575-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602575.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602574-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602574.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602590-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602590.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602591-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602591.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602606-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602606.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602607-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602607.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602587-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602587.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR5602586-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602586.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR2037123-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR2037123.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K39
cd SRR7630500-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR7630500.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/
# kmer=47
cd K47
cd ERR1917165-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR1917165.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602594-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602594.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602595-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602595.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602608-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602608.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602609-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602609.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602583-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602583.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602582-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602582.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602602-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602602.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602603-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602603.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd ERR964904-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR964904.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602589-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602589.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602588-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602588.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR6478596-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR6478596.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602584-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602584.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602585-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602585.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602605-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602605.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602604-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602604.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR4428742-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR4428742.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602576-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602576.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602577-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602577.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602593-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602593.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602592-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602592.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR2057084-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR2057084.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602599-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602599.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602598-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602598.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd ERR268390-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR268390.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR6932851-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR6932851.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602601-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602601.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602600-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602600.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602581-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602581.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602578-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602578.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602579-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602579.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5028199-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5028199.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602572-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602572.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602573-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602573.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602597-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602597.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602596-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602596.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602610-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602610.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR1145775-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR1145775.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd ERR2206741-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR2206741.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602575-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602575.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602574-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602574.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602590-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602590.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602591-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602591.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602606-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602606.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602607-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602607.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602587-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602587.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR5602586-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602586.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR2037123-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR2037123.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K47
cd SRR7630500-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR7630500.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/
# extra tests
# kmer=55
cd K55
cd ERR1917165-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR1917165.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602594-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602594.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602595-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602595.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602608-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602608.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602609-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602609.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602583-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602583.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602582-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602582.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602602-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602602.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602603-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602603.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd ERR964904-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR964904.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602589-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602589.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602588-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602588.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR6478596-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR6478596.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602584-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602584.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602585-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602585.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602605-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602605.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602604-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602604.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR4428742-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR4428742.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602576-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602576.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602577-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602577.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602593-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602593.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602592-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602592.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR2057084-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR2057084.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602599-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602599.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602598-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602598.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd ERR268390-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR268390.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR6932851-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR6932851.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602601-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602601.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602600-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602600.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602581-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602581.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602578-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602578.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602579-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602579.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5028199-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5028199.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602572-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602572.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602573-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602573.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602597-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602597.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602596-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602596.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602610-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602610.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR1145775-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR1145775.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd ERR2206741-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR2206741.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602575-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602575.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602574-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602574.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602590-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602590.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602591-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602591.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602606-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602606.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602607-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602607.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602587-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602587.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR5602586-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602586.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR2037123-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR2037123.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K55
cd SRR7630500-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR7630500.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/
# kmer=63
cd K63
cd ERR1917165-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR1917165.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602594-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602594.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602595-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602595.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602608-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602608.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602609-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602609.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602583-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602583.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602582-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602582.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602602-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602602.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602603-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602603.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd ERR964904-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR964904.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602589-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602589.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602588-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602588.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR6478596-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR6478596.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602584-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602584.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602585-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602585.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602605-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602605.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602604-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602604.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR4428742-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR4428742.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602576-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602576.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602577-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602577.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602593-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602593.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602592-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602592.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR2057084-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR2057084.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602599-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602599.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602598-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602598.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd ERR268390-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR268390.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR6932851-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR6932851.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602601-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602601.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602600-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602600.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602581-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602581.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602578-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602578.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602579-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602579.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5028199-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5028199.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602572-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602572.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602573-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602573.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602597-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602597.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602596-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602596.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602610-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602610.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR1145775-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR1145775.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd ERR2206741-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c ERR2206741.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602575-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602575.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602574-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602574.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602590-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602590.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602591-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602591.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602606-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602606.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602607-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602607.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602587-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602587.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR5602586-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR5602586.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR2037123-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR2037123.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/K63
cd SRR7630500-plastome
perl ../../../NOVOPlasty/NOVOPlasty2.7.2.pl -c SRR7630500.novoplasty.config.txt
cd ${RUN_PATH}/NOVOPlasty-plastome/
#
cd ${RUN_PATH}/NOVOPlasty-plastome/../