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4.evaluating_Published_plastomes.sh
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4.evaluating_Published_plastomes.sh
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evaluate_assembly_using_mapping.py -1 ERR1917165_1.fastq.gz -2 ERR1917165_2.fastq.gz -o Published-plastome/Published--ERR1917165-plastome--evaluated -f Published-plastome/ERR1917165.fasta --draw -c yes --plot-title ERR1917165-Published --plot-subtitle "Genbank accession: ERR1917165 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 ERR268390_1.fastq.gz -2 ERR268390_2.fastq.gz -o Published-plastome/Published--ERR268390-plastome--evaluated -f Published-plastome/HF937082.1.fasta --draw -c yes --plot-title ERR268390-Published --plot-subtitle "Genbank accession: HF937082.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 ERR964904_1.fastq.gz -2 ERR964904_2.fastq.gz -o Published-plastome/Published--ERR964904-plastome--evaluated -f Published-plastome/KT335971.1.fasta --draw -c yes --plot-title ERR964904-Published --plot-subtitle "Genbank accession: KT335971.1 Claimed status: circular genome" --plot-x-density 3000
evaluate_assembly_using_mapping.py -1 SRR1145775_1.fastq.gz -2 SRR1145775_2.fastq.gz -o Published-plastome/Published--SRR1145775-plastome--evaluated -f Published-plastome/KT378453.1.fasta --draw -c yes --plot-title SRR1145775-Published --plot-subtitle "Genbank accession: KT378453.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR2057084_1.fastq.gz -2 SRR2057084_2.fastq.gz -o Published-plastome/Published--SRR2057084-plastome--evaluated -f Published-plastome/KT595228.1.fasta --draw -c yes --plot-title SRR2057084-Published --plot-subtitle "Genbank accession: KT595228.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5028199_1.fastq.gz -2 SRR5028199_2.fastq.gz -o Published-plastome/Published--SRR5028199-plastome--evaluated -f Published-plastome/KU215903.2.fasta --draw -c yes --plot-title SRR5028199-Published --plot-subtitle "Genbank accession: KU215903.2 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602575_1.fastq.gz -2 SRR5602575_2.fastq.gz -o Published-plastome/Published--SRR5602575-plastome--evaluated -f Published-plastome/KX548217.1.fasta --draw -c yes --plot-title SRR5602575-Published --plot-subtitle "Genbank accession: KX548217.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602581_1.fastq.gz -2 SRR5602581_2.fastq.gz -o Published-plastome/Published--SRR5602581-plastome--evaluated -f Published-plastome/KX548219.1.fasta --draw -c yes --plot-title SRR5602581-Published --plot-subtitle "Genbank accession: KX548219.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602578_1.fastq.gz -2 SRR5602578_2.fastq.gz -o Published-plastome/Published--SRR5602578-plastome--evaluated -f Published-plastome/KX548220.1.fasta --draw -c yes --plot-title SRR5602578-Published --plot-subtitle "Genbank accession: KX548220.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602579_1.fastq.gz -2 SRR5602579_2.fastq.gz -o Published-plastome/Published--SRR5602579-plastome--evaluated -f Published-plastome/KX548221.1.fasta --draw -c yes --plot-title SRR5602579-Published --plot-subtitle "Genbank accession: KX548221.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602576_1.fastq.gz -2 SRR5602576_2.fastq.gz -o Published-plastome/Published--SRR5602576-plastome--evaluated -f Published-plastome/KX548222.1.fasta --draw -c yes --plot-title SRR5602576-Published --plot-subtitle "Genbank accession: KX548222.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602587_1.fastq.gz -2 SRR5602587_2.fastq.gz -o Published-plastome/Published--SRR5602587-plastome--evaluated -f Published-plastome/KX548223.1.fasta --draw -c yes --plot-title SRR5602587-Published --plot-subtitle "Genbank accession: KX548223.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602574_1.fastq.gz -2 SRR5602574_2.fastq.gz -o Published-plastome/Published--SRR5602574-plastome--evaluated -f Published-plastome/KX548224.1.fasta --draw -c yes --plot-title SRR5602574-Published --plot-subtitle "Genbank accession: KX548224.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602577_1.fastq.gz -2 SRR5602577_2.fastq.gz -o Published-plastome/Published--SRR5602577-plastome--evaluated -f Published-plastome/KX548225.1.fasta --draw -c yes --plot-title SRR5602577-Published --plot-subtitle "Genbank accession: KX548225.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR4428742_1.fastq.gz -2 SRR4428742_2.fastq.gz -o Published-plastome/Published--SRR4428742-plastome--evaluated -f Published-plastome/KX657870.1.fasta --draw -c yes --plot-title SRR4428742-Published --plot-subtitle "Genbank accession: KX657870.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602595_1.fastq.gz -2 SRR5602595_2.fastq.gz -o Published-plastome/Published--SRR5602595-plastome--evaluated -f Published-plastome/KY085890.1.fasta --draw -c yes --plot-title SRR5602595-Published --plot-subtitle "Genbank accession: KY085890.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602585_1.fastq.gz -2 SRR5602585_2.fastq.gz -o Published-plastome/Published--SRR5602585-plastome--evaluated -f Published-plastome/KY085891.1.fasta --draw -c yes --plot-title SRR5602585-Published --plot-subtitle "Genbank accession: KY085891.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602609_1.fastq.gz -2 SRR5602609_2.fastq.gz -o Published-plastome/Published--SRR5602609-plastome--evaluated -f Published-plastome/KY085892.1.fasta --draw -c yes --plot-title SRR5602609-Published --plot-subtitle "Genbank accession: KY085892.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602590_1.fastq.gz -2 SRR5602590_2.fastq.gz -o Published-plastome/Published--SRR5602590-plastome--evaluated -f Published-plastome/KY085893.1.fasta --draw -c yes --plot-title SRR5602590-Published --plot-subtitle "Genbank accession: KY085893.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602588_1.fastq.gz -2 SRR5602588_2.fastq.gz -o Published-plastome/Published--SRR5602588-plastome--evaluated -f Published-plastome/KY085894.1.fasta --draw -c yes --plot-title SRR5602588-Published --plot-subtitle "Genbank accession: KY085894.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602573_1.fastq.gz -2 SRR5602573_2.fastq.gz -o Published-plastome/Published--SRR5602573-plastome--evaluated -f Published-plastome/KY085895.1.fasta --draw -c yes --plot-title SRR5602573-Published --plot-subtitle "Genbank accession: KY085895.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602607_1.fastq.gz -2 SRR5602607_2.fastq.gz -o Published-plastome/Published--SRR5602607-plastome--evaluated -f Published-plastome/KY085896.1.fasta --draw -c yes --plot-title SRR5602607-Published --plot-subtitle "Genbank accession: KY085896.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602593_1.fastq.gz -2 SRR5602593_2.fastq.gz -o Published-plastome/Published--SRR5602593-plastome--evaluated -f Published-plastome/KY085897.1.fasta --draw -c yes --plot-title SRR5602593-Published --plot-subtitle "Genbank accession: KY085897.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602601_1.fastq.gz -2 SRR5602601_2.fastq.gz -o Published-plastome/Published--SRR5602601-plastome--evaluated -f Published-plastome/KY085898.1.fasta --draw -c yes --plot-title SRR5602601-Published --plot-subtitle "Genbank accession: KY085898.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602591_1.fastq.gz -2 SRR5602591_2.fastq.gz -o Published-plastome/Published--SRR5602591-plastome--evaluated -f Published-plastome/KY085899.1.fasta --draw -c yes --plot-title SRR5602591-Published --plot-subtitle "Genbank accession: KY085899.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602584_1.fastq.gz -2 SRR5602584_2.fastq.gz -o Published-plastome/Published--SRR5602584-plastome--evaluated -f Published-plastome/KY085900.1.fasta --draw -c yes --plot-title SRR5602584-Published --plot-subtitle "Genbank accession: KY085900.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602586_1.fastq.gz -2 SRR5602586_2.fastq.gz -o Published-plastome/Published--SRR5602586-plastome--evaluated -f Published-plastome/KY085901.1.fasta --draw -c yes --plot-title SRR5602586-Published --plot-subtitle "Genbank accession: KY085901.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602597_1.fastq.gz -2 SRR5602597_2.fastq.gz -o Published-plastome/Published--SRR5602597-plastome--evaluated -f Published-plastome/KY085903.1.fasta --draw -c yes --plot-title SRR5602597-Published --plot-subtitle "Genbank accession: KY085903.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602582_1.fastq.gz -2 SRR5602582_2.fastq.gz -o Published-plastome/Published--SRR5602582-plastome--evaluated -f Published-plastome/KY085904.1.fasta --draw -c yes --plot-title SRR5602582-Published --plot-subtitle "Genbank accession: KY085904.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602604_1.fastq.gz -2 SRR5602604_2.fastq.gz -o Published-plastome/Published--SRR5602604-plastome--evaluated -f Published-plastome/KY085905.1.fasta --draw -c yes --plot-title SRR5602604-Published --plot-subtitle "Genbank accession: KY085905.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602592_1.fastq.gz -2 SRR5602592_2.fastq.gz -o Published-plastome/Published--SRR5602592-plastome--evaluated -f Published-plastome/KY085906.1.fasta --draw -c yes --plot-title SRR5602592-Published --plot-subtitle "Genbank accession: KY085906.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602583_1.fastq.gz -2 SRR5602583_2.fastq.gz -o Published-plastome/Published--SRR5602583-plastome--evaluated -f Published-plastome/KY085907.1.fasta --draw -c yes --plot-title SRR5602583-Published --plot-subtitle "Genbank accession: KY085907.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602600_1.fastq.gz -2 SRR5602600_2.fastq.gz -o Published-plastome/Published--SRR5602600-plastome--evaluated -f Published-plastome/KY085908.1.fasta --draw -c yes --plot-title SRR5602600-Published --plot-subtitle "Genbank accession: KY085908.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602572_1.fastq.gz -2 SRR5602572_2.fastq.gz -o Published-plastome/Published--SRR5602572-plastome--evaluated -f Published-plastome/KY085909.1.fasta --draw -c yes --plot-title SRR5602572-Published --plot-subtitle "Genbank accession: KY085909.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602610_1.fastq.gz -2 SRR5602610_2.fastq.gz -o Published-plastome/Published--SRR5602610-plastome--evaluated -f Published-plastome/KY085910.1.fasta --draw -c yes --plot-title SRR5602610-Published --plot-subtitle "Genbank accession: KY085910.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602605_1.fastq.gz -2 SRR5602605_2.fastq.gz -o Published-plastome/Published--SRR5602605-plastome--evaluated -f Published-plastome/KY085911.1.fasta --draw -c yes --plot-title SRR5602605-Published --plot-subtitle "Genbank accession: KY085911.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602602_1.fastq.gz -2 SRR5602602_2.fastq.gz -o Published-plastome/Published--SRR5602602-plastome--evaluated -f Published-plastome/KY085912.1.fasta --draw -c yes --plot-title SRR5602602-Published --plot-subtitle "Genbank accession: KY085912.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602598_1.fastq.gz -2 SRR5602598_2.fastq.gz -o Published-plastome/Published--SRR5602598-plastome--evaluated -f Published-plastome/KY085913.1.fasta --draw -c yes --plot-title SRR5602598-Published --plot-subtitle "Genbank accession: KY085913.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602596_1.fastq.gz -2 SRR5602596_2.fastq.gz -o Published-plastome/Published--SRR5602596-plastome--evaluated -f Published-plastome/KY085914.1.fasta --draw -c yes --plot-title SRR5602596-Published --plot-subtitle "Genbank accession: KY085914.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602594_1.fastq.gz -2 SRR5602594_2.fastq.gz -o Published-plastome/Published--SRR5602594-plastome--evaluated -f Published-plastome/KY085915.1.fasta --draw -c yes --plot-title SRR5602594-Published --plot-subtitle "Genbank accession: KY085915.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602589_1.fastq.gz -2 SRR5602589_2.fastq.gz -o Published-plastome/Published--SRR5602589-plastome--evaluated -f Published-plastome/KY085916.1.fasta --draw -c yes --plot-title SRR5602589-Published --plot-subtitle "Genbank accession: KY085916.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602603_1.fastq.gz -2 SRR5602603_2.fastq.gz -o Published-plastome/Published--SRR5602603-plastome--evaluated -f Published-plastome/KY085917.1.fasta --draw -c yes --plot-title SRR5602603-Published --plot-subtitle "Genbank accession: KY085917.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602606_1.fastq.gz -2 SRR5602606_2.fastq.gz -o Published-plastome/Published--SRR5602606-plastome--evaluated -f Published-plastome/KY085918.1.fasta --draw -c yes --plot-title SRR5602606-Published --plot-subtitle "Genbank accession: KY085918.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602608_1.fastq.gz -2 SRR5602608_2.fastq.gz -o Published-plastome/Published--SRR5602608-plastome--evaluated -f Published-plastome/KY085919.1.fasta --draw -c yes --plot-title SRR5602608-Published --plot-subtitle "Genbank accession: KY085919.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR5602599_1.fastq.gz -2 SRR5602599_2.fastq.gz -o Published-plastome/Published--SRR5602599-plastome--evaluated -f Published-plastome/KY085920.1.fasta --draw -c yes --plot-title SRR5602599-Published --plot-subtitle "Genbank accession: KY085920.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR6932851_1.fastq.gz -2 SRR6932851_2.fastq.gz -o Published-plastome/Published--SRR6932851-plastome--evaluated -f Published-plastome/MF177094.1.fasta --draw -c yes --plot-title SRR6932851-Published --plot-subtitle "Genbank accession: MF177094.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR6478596_1.fastq.gz -2 SRR6478596_2.fastq.gz -o Published-plastome/Published--SRR6478596-plastome--evaluated -f Published-plastome/MF177095.1.fasta --draw -c yes --plot-title SRR6478596-Published --plot-subtitle "Genbank accession: MF177095.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR7630500_1.fastq.gz -2 SRR7630500_2.fastq.gz -o Published-plastome/Published--SRR7630500-plastome--evaluated -f Published-plastome/KP205433.1.fasta --draw -c yes --plot-title SRR7630500-Published --plot-subtitle "Genbank accession: KP205433.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 ERR2206741_1.fastq.gz -2 ERR2206741_2.fastq.gz -o Published-plastome/Published--ERR2206741-plastome--evaluated -f Published-plastome/MG922595.1.fasta --draw -c yes --plot-title ERR2206741-Published --plot-subtitle "Genbank accession: MG922595.1 Claimed status: circular genome"
evaluate_assembly_using_mapping.py -1 SRR2037123_1.fastq.gz -2 SRR2037123_2.fastq.gz -o Published-plastome/Published--SRR2037123-plastome--evaluated -f Published-plastome/MH549643.1.fasta --draw -c yes --plot-title SRR2037123-Published --plot-subtitle "Genbank accession: MH549643.1 Claimed status: circular genome"