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5-1.assembling_56_animal_mitogenomes_using_GetOrganelle.sh
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5-1.assembling_56_animal_mitogenomes_using_GetOrganelle.sh
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get_organelle_from_reads.py -1 DRR014695_1.fastq.gz -2 DRR014695_2.fastq.gz -F animal_mt -o auto--DRR014695-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 DRR095708_1.fastq.gz -2 DRR095708_2.fastq.gz -F animal_mt -o auto--DRR095708-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 ERR1856354_1.fastq.gz -2 ERR1856354_2.fastq.gz -F animal_mt -o auto--ERR1856354-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 ERR1952738_1.fastq.gz -2 ERR1952738_2.fastq.gz -F animal_mt -o auto--ERR1952738-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 ERR466754_1.fastq.gz -2 ERR466754_2.fastq.gz -F animal_mt -o auto--ERR466754-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR039541_1.fastq.gz -2 SRR039541_2.fastq.gz -F animal_mt -o auto--SRR039541-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR1041081_1.fastq.gz -2 SRR1041081_2.fastq.gz -F animal_mt -o auto--SRR1041081-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR1055280_1.fastq.gz -2 SRR1055280_2.fastq.gz -F animal_mt -o auto--SRR1055280-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR1200276_1.fastq.gz -2 SRR1200276_2.fastq.gz -F animal_mt -o auto--SRR1200276-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR1284940_1.fastq.gz -2 SRR1284940_2.fastq.gz -F animal_mt -o auto--SRR1284940-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR1298377_1.fastq.gz -2 SRR1298377_2.fastq.gz -F animal_mt -o auto--SRR1298377-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR1300141_1.fastq.gz -2 SRR1300141_2.fastq.gz -F animal_mt -o auto--SRR1300141-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR136494_1.fastq.gz -2 SRR136494_2.fastq.gz -F animal_mt -o auto--SRR136494-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR1566160_1.fastq.gz -2 SRR1566160_2.fastq.gz -F animal_mt -o auto--SRR1566160-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR1581065_1.fastq.gz -2 SRR1581065_2.fastq.gz -F animal_mt -o auto--SRR1581065-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR1657027_1.fastq.gz -2 SRR1657027_2.fastq.gz -F animal_mt -o auto--SRR1657027-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR1743021_1.fastq.gz -2 SRR1743021_2.fastq.gz -F animal_mt -o auto--SRR1743021-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR1822107_1.fastq.gz -2 SRR1822107_2.fastq.gz -F animal_mt -o auto--SRR1822107-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR1946581_1.fastq.gz -2 SRR1946581_2.fastq.gz -F animal_mt -o auto--SRR1946581-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR1950515_1.fastq.gz -2 SRR1950515_2.fastq.gz -F animal_mt -o auto--SRR1950515-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR2132981_1.fastq.gz -2 SRR2132981_2.fastq.gz -F animal_mt -o auto--SRR2132981-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR2179962_1.fastq.gz -2 SRR2179962_2.fastq.gz -F animal_mt -o auto--SRR2179962-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR2318706_1.fastq.gz -2 SRR2318706_2.fastq.gz -F animal_mt -o auto--SRR2318706-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR2717571_1.fastq.gz -2 SRR2717571_2.fastq.gz -F animal_mt -o auto--SRR2717571-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR2730309_1.fastq.gz -2 SRR2730309_2.fastq.gz -F animal_mt -o auto--SRR2730309-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR2737540_1.fastq.gz -2 SRR2737540_2.fastq.gz -F animal_mt -o auto--SRR2737540-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR3041429_1.fastq.gz -2 SRR3041429_2.fastq.gz -F animal_mt -o auto--SRR3041429-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR305235_1.fastq.gz -2 SRR305235_2.fastq.gz -F animal_mt -o auto--SRR305235-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR3098386_1.fastq.gz -2 SRR3098386_2.fastq.gz -F animal_mt -o auto--SRR3098386-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR329682_1.fastq.gz -2 SRR329682_2.fastq.gz -F animal_mt -o auto--SRR329682-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR3879971_1.fastq.gz -2 SRR3879971_2.fastq.gz -F animal_mt -o auto--SRR3879971-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR3953043_1.fastq.gz -2 SRR3953043_2.fastq.gz -F animal_mt -o auto--SRR3953043-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR4095109_1.fastq.gz -2 SRR4095109_2.fastq.gz -F animal_mt -o auto--SRR4095109-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR4339879_1.fastq.gz -2 SRR4339879_2.fastq.gz -F animal_mt -o auto--SRR4339879-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR4340274_1.fastq.gz -2 SRR4340274_2.fastq.gz -F animal_mt -o auto--SRR4340274-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR4782254_1.fastq.gz -2 SRR4782254_2.fastq.gz -F animal_mt -o auto--SRR4782254-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5056303_1.fastq.gz -2 SRR5056303_2.fastq.gz -F animal_mt -o auto--SRR5056303-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5132384_1.fastq.gz -2 SRR5132384_2.fastq.gz -F animal_mt -o auto--SRR5132384-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5201683_1.fastq.gz -2 SRR5201683_2.fastq.gz -F animal_mt -o auto--SRR5201683-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5495100_1.fastq.gz -2 SRR5495100_2.fastq.gz -F animal_mt -o auto--SRR5495100-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5527082_1.fastq.gz -2 SRR5527082_2.fastq.gz -F animal_mt -o auto--SRR5527082-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5620467_1.fastq.gz -2 SRR5620467_2.fastq.gz -F animal_mt -o auto--SRR5620467-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5769010_1.fastq.gz -2 SRR5769010_2.fastq.gz -F animal_mt -o auto--SRR5769010-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5860573_1.fastq.gz -2 SRR5860573_2.fastq.gz -F animal_mt -o auto--SRR5860573-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5863004_1.fastq.gz -2 SRR5863004_2.fastq.gz -F animal_mt -o auto--SRR5863004-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5875655_1.fastq.gz -2 SRR5875655_2.fastq.gz -F animal_mt -o auto--SRR5875655-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR5878339_1.fastq.gz -2 SRR5878339_2.fastq.gz -F animal_mt -o auto--SRR5878339-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR611174_1.fastq.gz -2 SRR611174_2.fastq.gz -F animal_mt -o auto--SRR611174-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR620242_1.fastq.gz -2 SRR620242_2.fastq.gz -F animal_mt -o auto--SRR620242-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR747928_1.fastq.gz -2 SRR747928_2.fastq.gz -F animal_mt -o auto--SRR747928-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR748049_1.fastq.gz -2 SRR748049_2.fastq.gz -F animal_mt -o auto--SRR748049-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR836315_1.fastq.gz -2 SRR836315_2.fastq.gz -F animal_mt -o auto--SRR836315-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR847379_1.fastq.gz -2 SRR847379_2.fastq.gz -F animal_mt -o auto--SRR847379-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR940268_1.fastq.gz -2 SRR940268_2.fastq.gz -F animal_mt -o auto--SRR940268-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR941879_1.fastq.gz -2 SRR941879_2.fastq.gz -F animal_mt -o auto--SRR941879-mitogenome -R 10 -t 1 -k 21,43,65,87,127
get_organelle_from_reads.py -1 SRR955308_1.fastq.gz -2 SRR955308_2.fastq.gz -F animal_mt -o auto--SRR955308-mitogenome -R 10 -t 1 -k 21,43,65,87,127
mkdir GetOrganelle-animal-mitogenome
mv *mitogenome GetOrganelle-animal-mitogenome