cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_10V-TomD_LynchAB_RP4.read1.paired.fastq.gz --pe1-2 Sample_10V-TomD_LynchAB_RP4.read2.paired.fastq.gz -t 16 -o Sample_10V-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_12V-TomD_LynchAB_RP4.read1.paired.fastq.gz --pe1-2 Sample_12V-TomD_LynchAB_RP4.read2.paired.fastq.gz -t 16 -o Sample_12V-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_1D1-TomD_LynchAB_RP4.read1.paired.fastq.gz --pe1-2 Sample_1D1-TomD_LynchAB_RP4.read2.paired.fastq.gz -t 16 -o Sample_1D1-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_209-TomD_Lynch100514Set2.read1.paired.fastq.gz --pe1-2 Sample_209-TomD_Lynch100514Set2.read2.paired.fastq.gz -t 16 -o Sample_209-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_219-11-TomD_Lynch100514Set1.read1.paired.fastq.gz --pe1-2 Sample_219-11-TomD_Lynch100514Set1.read2.paired.fastq.gz -t 16 -o Sample_219-11-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_223-TomD_Lynch100514Set1.read1.paired.fastq.gz --pe1-2 Sample_223-TomD_Lynch100514Set1.read2.paired.fastq.gz -t 16 -o Sample_223-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_23Maymale13515-TomD_Lynch100514Set1.read1.paired.fastq.gz --pe1-2 Sample_23Maymale13515-TomD_Lynch100514Set1.read2.paired.fastq.gz -t 16 -o Sample_23Maymale13515-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_4D_2_14_16_12-TomD_LynchAB_RP4.read1.paired.fastq.gz --pe1-2 Sample_4D_2_14_16_12-TomD_LynchAB_RP4.read2.paired.fastq.gz -t 16 -o Sample_4D_2_14_16_12-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_4D_2_24_16_12-TomD_LynchAB_RP4.read1.paired.fastq.gz --pe1-2 Sample_4D_2_24_16_12-TomD_LynchAB_RP4.read2.paired.fastq.gz -t 16 -o Sample_4D_2_24_16_12-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_5JunePE13515-TomD_Lynch100514Set1.read1.paired.fastq.gz --pe1-2 Sample_5JunePE13515-TomD_Lynch100514Set1.read2.paired.fastq.gz -t 16 -o Sample_5JunePE13515-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_858-TomD_Lynch100514Set2.read1.paired.fastq.gz --pe1-2 Sample_858-TomD_Lynch100514Set2.read2.paired.fastq.gz -t 16 -o Sample_858-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_9June1A13515-TomD_Lynch100514Set2.read1.paired.fastq.gz --pe1-2 Sample_9June1A13515-TomD_Lynch100514Set2.read2.paired.fastq.gz -t 16 -o Sample_9June1A13515-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_A39-TomD_LynchAB_RP4.read1.paired.fastq.gz --pe1-2 Sample_A39-TomD_LynchAB_RP4.read2.paired.fastq.gz -t 16 -o Sample_A39-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_BM4-1-TomD_Lynch100514Set1.read1.paired.fastq.gz --pe1-2 Sample_BM4-1-TomD_Lynch100514Set1.read2.paired.fastq.gz -t 16 -o Sample_BM4-1-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_dec-TomD_Lynch100514Set1.read1.paired.fastq.gz --pe1-2 Sample_dec-TomD_Lynch100514Set1.read2.paired.fastq.gz -t 16 -o Sample_dec-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_K12-TomD_Lynch100514Set1.read1.paired.fastq.gz --pe1-2 Sample_K12-TomD_Lynch100514Set1.read2.paired.fastq.gz -t 16 -o Sample_K12-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_K412-TomD_LynchAB_RP4.read1.paired.fastq.gz --pe1-2 Sample_K412-TomD_LynchAB_RP4.read2.paired.fastq.gz -t 16 -o Sample_K412-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_M-TomD_Lynch100514Set1.read1.paired.fastq.gz --pe1-2 Sample_M-TomD_Lynch100514Set1.read2.paired.fastq.gz -t 16 -o Sample_M-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_MA-TomD_Lynch100514Set2.read1.paired.fastq.gz --pe1-2 Sample_MA-TomD_Lynch100514Set2.read2.paired.fastq.gz -t 16 -o Sample_MA-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_ovt-TomD_Lynch100514Set1.read1.paired.fastq.gz --pe1-2 Sample_ovt-TomD_Lynch100514Set1.read2.paired.fastq.gz -t 16 -o Sample_ovt-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_PB-TomD_Lynch100514Set1.read1.paired.fastq.gz --pe1-2 Sample_PB-TomD_Lynch100514Set1.read2.paired.fastq.gz -t 16 -o Sample_PB-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_PbU4-1-TomD_Lynch100514Set2.read1.paired.fastq.gz --pe1-2 Sample_PbU4-1-TomD_Lynch100514Set2.read2.paired.fastq.gz -t 16 -o Sample_PbU4-1-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_PO-TomD_Lynch100514Set2.read1.paired.fastq.gz --pe1-2 Sample_PO-TomD_Lynch100514Set2.read2.paired.fastq.gz -t 16 -o Sample_PO-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_Psonn-TomD_Lynch100514Set2.read1.paired.fastq.gz --pe1-2 Sample_Psonn-TomD_Lynch100514Set2.read2.paired.fastq.gz -t 16 -o Sample_Psonn-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_TE2-16-TomD_Lynch100514Set2.read1.paired.fastq.gz --pe1-2 Sample_TE2-16-TomD_Lynch100514Set2.read2.paired.fastq.gz -t 16 -o Sample_TE2-16-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-05-27-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 Sample_227-TomD_Lynch100514Set1.read1.paired.fastq.gz --pe1-2 Sample_227-TomD_Lynch100514Set1.read1.paired.fastq.gz --pe2-1 Sample_227-TomD_LynchAB_RP4.read1.paired.fastq.gz --pe2-2 Sample_227-TomD_LynchAB_RP4.read2.paired.fastq.gz -t 16 -o Sample_227-SPAdes-3.5.0-trimmed