cd /N/dc2/projects/marinovg/2016-01-01-november-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_209-209_TCCGCGAA-CCTATCCT_L001_R1_all.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_209-209_TCCGCGAA-CCTATCCT_L001_R2_all.paired.fastq.gz --mp1-1 GSF816-Doak-209-not-good_S97_R1_001.paired.fastq.gz --mp1-2 GSF816-Doak-209-not-good_S97_R2_001.paired.fastq.gz -t 16 -o Sample_209-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2016-01-01-november-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_223-223_CGGCTATG-GGCTCTGA_L002_R1_all.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_223-223_CGGCTATG-GGCTCTGA_L002_R2_all.paired.fastq.gz --mp1-1 GSF816-Doak-223-10k_S98_R1_001.paired.fastq.gz --mp1-2 GSF816-Doak-223-10k_S98_R2_001.paired.fastq.gz --mp2-1 GSF816-Doak-223-6k_S99_R1_001.paired.fastq.gz --mp2-2 GSF816-Doak-223-6k_S99_R2_001.paired.fastq.gz -t 16 -o Sample_223-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2016-01-01-november-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_227-227_TCCGCGAA-AGGCGAAG_L002_R1_all.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_227-227_TCCGCGAA-AGGCGAAG_L002_R2_all.paired.fastq.gz --mp1-1 GSF816-Doak-227_S100_R1_001.paired.fastq.gz --mp1-2 GSF816-Doak-227_S100_R2_001.paired.fastq.gz -t 16 -o Sample_227-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2016-01-01-november-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_M-M_CGGCTATG-GTACTGAC_L002_R1_all.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_M-M_CGGCTATG-GTACTGAC_L002_R2_all.paired.fastq.gz --mp1-1 GSF816-Doak-M-6k_S103_R1_001.paired.fastq.gz --mp1-2 GSF816-Doak-M-6k_S103_R2_001.paired.fastq.gz --mp2-1 GSF816-Doak-M-7k_S104_R1_001.paired.fastq.gz --mp2-2 GSF816-Doak-M-7k_S104_R2_001.paired.fastq.gz -t 16 -o Sample_M-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2016-01-01-november-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_K12-K12_TCCGCGAA-CAGGACGT_L002_R1_all.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_K12-K12_TCCGCGAA-CAGGACGT_L002_R2_all.paired.fastq.gz --mp1-1 GSF816-Doak-K12_S102_R1_001.paired.fastq.gz --mp1-2 GSF816-Doak-K12_S102_R2_001.paired.fastq.gz -t 16 -o  Sample_K12-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2016-01-01-november-data; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_Psonn-Psonn_CGGCTATG-AGGCGAAG_L001_R1_all.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-06-23-data/pooled-reads/Sample_Psonn-Psonn_CGGCTATG-AGGCGAAG_L001_R2_all.paired.fastq.gz --mp1-1 GSF816-Doak-Psonn-5k_S107_R1_001.paired.fastq.gz --mp1-2 GSF816-Doak-Psonn-5k_S107_R2_001.paired.fastq.gz --mp2-1 GSF816-Doak-Psonn-7k_S108_R1_001.paired.fastq.gz --mp2-2 GSF816-Doak-Psonn-7k_S108_R2_001.paired.fastq.gz -t 16 -o Sample_Psonn-SPAdes-3.5.0-trimmed