cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_256-UB2/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_256-UB2/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_256-UB2/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_256-UB2/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_256-UB2/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_256-UB2/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_258-UB4/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_258-UB4/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_258-UB4/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_258-UB4/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_258-UB4/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_258-UB4/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_31/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_31/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_31/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_31/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_31/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_31/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_379/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_379/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_379/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_379/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_379/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_379/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_44/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_44/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_44/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_44/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_44/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_44/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_45/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_45/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_45/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_45/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_45/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_45/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_562alpha/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_562alpha/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_562alpha/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_562alpha/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_562alpha/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_562alpha/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_76/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_76/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_76/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_76/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_76/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_76/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_7K/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_7K/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_7K/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_7K/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_7K/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_7K/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C023/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C023/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C023/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C023/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C023/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C023/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C033/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C033/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C033/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C033/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C033/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C033/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C065/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C065/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C065/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C065/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C065/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C065/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C083/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C083/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C083/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C083/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C083/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C083/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C104/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C104/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C104/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C104/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C104/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C104/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C119/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C119/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C119/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C119/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C119/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C119/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C131/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C131/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C131/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C131/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C131/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C131/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C147/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C147/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C147/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C147/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C147/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C147/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M03/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M03/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M03/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M03/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M03/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M03/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M04/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M04/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M04/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M04/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M04/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M04/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M05/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M05/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M05/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M05/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M05/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M05/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M09/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M09/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M09/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M09/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M09/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M09/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M12/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M12/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M12/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M12/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M12/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M12/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.octaurelia-Sample_1038/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.octaurelia-Sample_1038/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.octaurelia-Sample_1038/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.octaurelia-Sample_1038/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.octaurelia-Sample_1038/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.octaurelia-Sample_1038/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_126/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_126/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_126/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_126/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_126/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_126/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_128/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_128/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_128/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_128/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_128/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_128/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_130/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_130/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_130/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_130/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_130/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_130/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_265/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_265/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_265/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_265/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_265/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_265/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_169/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_169/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_169/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_169/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_169/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_169/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_291/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_291/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_291/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_291/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_291/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_291/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_298/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_298/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_298/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_298/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_298/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_298/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_47/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_47/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_47/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_47/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_47/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_47/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_51/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_51/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_51/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_51/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_51/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_51/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_98/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_98/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_98/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_98/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_98/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_98/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_99/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_99/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_99/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_99/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_99/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_99/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A30/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A30/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A30/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A30/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A30/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A30/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_B/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_B/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_B/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_B/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_B/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_B/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_M02/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_M02/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_M02/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_M02/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_M02/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_M02/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Canal-1I/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Canal-1I/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Canal-1I/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Canal-1I/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Canal-1I/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Canal-1I/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_TRB101-4/reads.end1.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_TRB101-4/reads.end2.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_TRB101-4/reads.end1.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_TRB101-4/reads.end1.unpaired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_TRB101-4/reads.end2.paired.fastq.gz /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_TRB101-4/reads.end2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &