java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE /oak/stanford/groups/akundaje/marinovg/Symbiodinium/WGS-data/SSBO1_reads/130725_TENNISON_0237_BD29AFACXX_L1_TAGGCATG-AGAGTAGA_1_pf.fastq.gz /oak/stanford/groups/akundaje/marinovg/Symbiodinium/WGS-data/SSBO1_reads/130725_TENNISON_0237_BD29AFACXX_L1_TAGGCATG-AGAGTAGA_2_pf.fastq.gz SSBO1.read1.paired.fastq.gz SSBO1.read1.unpaired.fastq.gz SSBO1.read2.paired.fastq.gz SSBO1.read2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &
java -jar /oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE /oak/stanford/groups/akundaje/marinovg/Symbiodinium/WGS-data/SSAO1_reads/SCGPM_SSA01-SSE01-genomic_HL72T_L1_TAAGGCGA-AGAGGATA_R1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Symbiodinium/WGS-data/SSAO1_reads/SCGPM_SSA01-SSE01-genomic_HL72T_L1_TAAGGCGA-AGAGGATA_R2.fastq.gz SSA01-SSE01-genomic_HL72T.read1.paired.fastq.gz SSA01-SSE01-genomic_HL72T.read1.unpaired.fastq.gz SSA01-SSE01-genomic_HL72T.read2.paired.fastq.gz SSA01-SSE01-genomic_HL72T.read2.unpaired.fastq.gz ILLUMINACLIP:/oak/stanford/groups/akundaje/marinovg/programs/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &