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6-1.assembling_50_fungal_mitogenomes_using_GetOrganelle.sh
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6-1.assembling_50_fungal_mitogenomes_using_GetOrganelle.sh
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get_organelle_from_reads.py -1 SRR5754079_1.fastq.gz -2 SRR5754079_2.fastq.gz -F fungus_mt -o auto--SRR5754079-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5764827_1.fastq.gz -2 SRR5764827_2.fastq.gz -F fungus_mt -o auto--SRR5764827-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5764829_1.fastq.gz -2 SRR5764829_2.fastq.gz -F fungus_mt -o auto--SRR5764829-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5764835_1.fastq.gz -2 SRR5764835_2.fastq.gz -F fungus_mt -o auto--SRR5764835-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5765276_1.fastq.gz -2 SRR5765276_2.fastq.gz -F fungus_mt -o auto--SRR5765276-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5765278_1.fastq.gz -2 SRR5765278_2.fastq.gz -F fungus_mt -o auto--SRR5765278-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5801929_1.fastq.gz -2 SRR5801929_2.fastq.gz -F fungus_mt -o auto--SRR5801929-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5801932_1.fastq.gz -2 SRR5801932_2.fastq.gz -F fungus_mt -o auto--SRR5801932-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5801933_1.fastq.gz -2 SRR5801933_2.fastq.gz -F fungus_mt -o auto--SRR5801933-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5801934_1.fastq.gz -2 SRR5801934_2.fastq.gz -F fungus_mt -o auto--SRR5801934-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5801935_1.fastq.gz -2 SRR5801935_2.fastq.gz -F fungus_mt -o auto--SRR5801935-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5801943_1.fastq.gz -2 SRR5801943_2.fastq.gz -F fungus_mt -o auto--SRR5801943-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5801947_1.fastq.gz -2 SRR5801947_2.fastq.gz -F fungus_mt -o auto--SRR5801947-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5802125_1.fastq.gz -2 SRR5802125_2.fastq.gz -F fungus_mt -o auto--SRR5802125-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5802181_1.fastq.gz -2 SRR5802181_2.fastq.gz -F fungus_mt -o auto--SRR5802181-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5802411_1.fastq.gz -2 SRR5802411_2.fastq.gz -F fungus_mt -o auto--SRR5802411-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5802413_1.fastq.gz -2 SRR5802413_2.fastq.gz -F fungus_mt -o auto--SRR5802413-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5802419_1.fastq.gz -2 SRR5802419_2.fastq.gz -F fungus_mt -o auto--SRR5802419-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5802698_1.fastq.gz -2 SRR5802698_2.fastq.gz -F fungus_mt -o auto--SRR5802698-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5803890_1.fastq.gz -2 SRR5803890_2.fastq.gz -F fungus_mt -o auto--SRR5803890-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5803905_1.fastq.gz -2 SRR5803905_2.fastq.gz -F fungus_mt -o auto--SRR5803905-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5803909_1.fastq.gz -2 SRR5803909_2.fastq.gz -F fungus_mt -o auto--SRR5803909-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5803913_1.fastq.gz -2 SRR5803913_2.fastq.gz -F fungus_mt -o auto--SRR5803913-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5803916_1.fastq.gz -2 SRR5803916_2.fastq.gz -F fungus_mt -o auto--SRR5803916-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5803922_1.fastq.gz -2 SRR5803922_2.fastq.gz -F fungus_mt -o auto--SRR5803922-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5803923_1.fastq.gz -2 SRR5803923_2.fastq.gz -F fungus_mt -o auto--SRR5803923-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5803926_1.fastq.gz -2 SRR5803926_2.fastq.gz -F fungus_mt -o auto--SRR5803926-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5803928_1.fastq.gz -2 SRR5803928_2.fastq.gz -F fungus_mt -o auto--SRR5803928-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5803930_1.fastq.gz -2 SRR5803930_2.fastq.gz -F fungus_mt -o auto--SRR5803930-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5803933_1.fastq.gz -2 SRR5803933_2.fastq.gz -F fungus_mt -o auto--SRR5803933-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804015_1.fastq.gz -2 SRR5804015_2.fastq.gz -F fungus_mt -o auto--SRR5804015-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804017_1.fastq.gz -2 SRR5804017_2.fastq.gz -F fungus_mt -o auto--SRR5804017-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804018_1.fastq.gz -2 SRR5804018_2.fastq.gz -F fungus_mt -o auto--SRR5804018-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804020_1.fastq.gz -2 SRR5804020_2.fastq.gz -F fungus_mt -o auto--SRR5804020-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804023_1.fastq.gz -2 SRR5804023_2.fastq.gz -F fungus_mt -o auto--SRR5804023-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804112_1.fastq.gz -2 SRR5804112_2.fastq.gz -F fungus_mt -o auto--SRR5804112-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804115_1.fastq.gz -2 SRR5804115_2.fastq.gz -F fungus_mt -o auto--SRR5804115-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804118_1.fastq.gz -2 SRR5804118_2.fastq.gz -F fungus_mt -o auto--SRR5804118-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804119_1.fastq.gz -2 SRR5804119_2.fastq.gz -F fungus_mt -o auto--SRR5804119-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804120_1.fastq.gz -2 SRR5804120_2.fastq.gz -F fungus_mt -o auto--SRR5804120-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804127_1.fastq.gz -2 SRR5804127_2.fastq.gz -F fungus_mt -o auto--SRR5804127-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804130_1.fastq.gz -2 SRR5804130_2.fastq.gz -F fungus_mt -o auto--SRR5804130-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804131_1.fastq.gz -2 SRR5804131_2.fastq.gz -F fungus_mt -o auto--SRR5804131-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804137_1.fastq.gz -2 SRR5804137_2.fastq.gz -F fungus_mt -o auto--SRR5804137-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804139_1.fastq.gz -2 SRR5804139_2.fastq.gz -F fungus_mt -o auto--SRR5804139-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804145_1.fastq.gz -2 SRR5804145_2.fastq.gz -F fungus_mt -o auto--SRR5804145-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804147_1.fastq.gz -2 SRR5804147_2.fastq.gz -F fungus_mt -o auto--SRR5804147-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804153_1.fastq.gz -2 SRR5804153_2.fastq.gz -F fungus_mt -o auto--SRR5804153-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804157_1.fastq.gz -2 SRR5804157_2.fastq.gz -F fungus_mt -o auto--SRR5804157-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5804159_1.fastq.gz -2 SRR5804159_2.fastq.gz -F fungus_mt -o auto--SRR5804159-mitogenome -R 10 -t 1 -k 21,43,65,87,127
mkdir GetOrganelle-fungal-mitogenome
mv *mitogenome GetOrganelle-fungal-mitogenome