cd /N/dc2/projects/marinovg/2015-10-29-Haemophilus_ducreyi; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE IB0001_1.fastq.gz IB0001_2.fastq.gz IB0001_1.paired.fastq.gz IB0001_1.unpaired.fastq.gz IB0001_2.paired.fastq.gz IB0001_2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/TruSeq2-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-10-29-Haemophilus_ducreyi; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE IB0001_1.150mers.fastq.gz IB0001_2.150mers.fastq.gz IB0001_1.150mers.paired.fastq.gz IB0001_1.150mers.unpaired.fastq.gz IB0001_2.150mers.paired.fastq.gz IB0001_2.150mers.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/TruSeq2-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2015-10-29-Haemophilus_ducreyi; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE IB0001_1.mid150mers.fastq.gz IB0001_2.mid150mers.fastq.gz IB0001_1.mid150mers.paired.fastq.gz IB0001_1.mid150mers.unpaired.fastq.gz IB0001_2.mid150mers.paired.fastq.gz IB0001_2.mid150mers.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/TruSeq2-PE.fa:2:30:10 &