python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R1.trimmed.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R2.trimmed.paired.fastq.gz --pe2-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R1.trimmed.paired.fastq.gz --pe2-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R2.trimmed.paired.fastq.gz --pe3-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R1.trimmed.paired.fastq.gz --pe3-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R2.trimmed.paired.fastq.gz --pe4-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R1.trimmed.paired.fastq.gz --pe4-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R2.trimmed.paired.fastq.gz --mp1-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R1.trimmed.paired.fastq.gz --mp1-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R2.trimmed.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed
python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --mp1-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_87E-553MP-130405_M01529_0005_Lynch553MP.R1.trimmed.paired.fastq.gz--mp1-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_87E-553MP-130405_M01529_0005_Lynch553MP.R2.trimmed.paired.fastq.gz --pe1-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_87E-553short-130405_M01529_0005_Lynch553short.R1.trimmed.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_87E-553short-130405_M01529_0005_Lynch553short.R2.trimmed.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_87E-SPAdes-3.5.0-trimmed
python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/jenningsi-strain_M-Run_141105-M_CGGCTATG-GTACTGAC_L001_R1_001.trimmed.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/jenningsi-strain_M-Run_141105-M_CGGCTATG-GTACTGAC_L001_R2_001.trimmed.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_jenningsi-SPAdes-3.5.0-trimmed
python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/undecaurelia-strain_AP58-Run_141105-219-11_CGGCTATG-ATAGAGGC_L001_R1_001.trimmed.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/undecaurelia-strain_AP58-Run_141105-219-11_CGGCTATG-ATAGAGGC_L001_R2_001.trimmed.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_undecaurelia-SPAdes-3.5.0-trimmed
python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/sonneborni-AP59-Run_141105-Psonn_CGGCTATG-AGGCGAAG_L001_R1_001.trimmed.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/sonneborni-AP59-Run_141105-Psonn_CGGCTATG-AGGCGAAG_L001_R2_001.trimmed.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_sonneborni-SPAdes-3.5.0-trimmed
python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/putrinum-strain_BM4-1-Run_141105-BM4-1_CGGCTATG-CCTATCCT_L001_R1_001.trimmed.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/putrinum-strain_BM4-1-Run_141105-BM4-1_CGGCTATG-CCTATCCT_L001_R2_001.trimmed.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_putrinum-SPAdes-3.5.0-trimmed
python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/septaurelia-strain_227-Run_141105-227_TCCGCGAA-AGGCGAAG_L001_R1_001.trimmed.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/septaurelia-strain_227-Run_141105-227_TCCGCGAA-AGGCGAAG_L001_R2_001.trimmed.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_septaurelia-SPAdes-3.5.0-trimmed
python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/decaurelia-strain_223-Run_141105-223_CGGCTATG-GGCTCTGA_L001_R1_001.trimmed.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/decaurelia-strain_223-Run_141105-223_CGGCTATG-GGCTCTGA_L001_R2_001.trimmed.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_decaurelia-SPAdes-3.5.0-trimmed