<commit_before>trimmomatic PE -phred33 reads/SS.11.01_1.fq.gz reads/SS.11.01_2.fq.gz -baseout TRIM/SS.11.01.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.02_1.fq.gz reads/SS.11.02_2.fq.gz -baseout TRIM/SS.11.02.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.03_1.fq.gz reads/SS.11.03_2.fq.gz -baseout TRIM/SS.11.03.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.04_1.fq.gz reads/SS.11.04_2.fq.gz -baseout TRIM/SS.11.04.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.05_1.fq.gz reads/SS.11.05_2.fq.gz -baseout TRIM/SS.11.05.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.06_1.fq.gz reads/SS.11.06_2.fq.gz -baseout TRIM/SS.11.06.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.07_1.fq.gz reads/SS.11.07_2.fq.gz -baseout TRIM/SS.11.07.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.08_1.fq.gz reads/SS.11.08_2.fq.gz -baseout TRIM/SS.11.08.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.09_1.fq.gz reads/SS.11.09_2.fq.gz -baseout TRIM/SS.11.09.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.10_1.fq.gz reads/SS.11.10_2.fq.gz -baseout TRIM/SS.11.10.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.11_1.fq.gz reads/SS.11.11_2.fq.gz -baseout TRIM/SS.11.11.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.12_1.fq.gz reads/SS.11.12_2.fq.gz -baseout TRIM/SS.11.12.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.13_1.fq.gz reads/SS.11.13_2.fq.gz -baseout TRIM/SS.11.13.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.14_1.fq.gz reads/SS.11.14_2.fq.gz -baseout TRIM/SS.11.14.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.15_1.fq.gz reads/SS.11.15_2.fq.gz -baseout TRIM/SS.11.15.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.16_1.fq.gz reads/SS.11.16_2.fq.gz -baseout TRIM/SS.11.16.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.17_1.fq.gz reads/SS.11.17_2.fq.gz -baseout TRIM/SS.11.17.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.18_1.fq.gz reads/SS.11.18_2.fq.gz -baseout TRIM/SS.11.18.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.19_1.fq.gz reads/SS.11.19_2.fq.gz -baseout TRIM/SS.11.19.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.20_1.fq.gz reads/SS.11.20_2.fq.gz -baseout TRIM/SS.11.20.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.21_1.fq.gz reads/SS.11.21_2.fq.gz -baseout TRIM/SS.11.21.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.22_1.fq.gz reads/SS.11.22_2.fq.gz -baseout TRIM/SS.11.22.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.23_1.fq.gz reads/SS.11.23_2.fq.gz -baseout TRIM/SS.11.23.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.24_1.fq.gz reads/SS.11.24_2.fq.gz -baseout TRIM/SS.11.24.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.25_1.fq.gz reads/SS.11.25_2.fq.gz -baseout TRIM/SS.11.25.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.26_1.fq.gz reads/SS.11.26_2.fq.gz -baseout TRIM/SS.11.26.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.27_1.fq.gz reads/SS.11.27_2.fq.gz -baseout TRIM/SS.11.27.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.28_1.fq.gz reads/SS.11.28_2.fq.gz -baseout TRIM/SS.11.28.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.29_1.fq.gz reads/SS.11.29_2.fq.gz -baseout TRIM/SS.11.29.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.30_1.fq.gz reads/SS.11.30_2.fq.gz -baseout TRIM/SS.11.30.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.31_1.fq.gz reads/SS.11.31_2.fq.gz -baseout TRIM/SS.11.31.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.32_1.fq.gz reads/SS.11.32_2.fq.gz -baseout TRIM/SS.11.32.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.33_1.fq.gz reads/SS.11.33_2.fq.gz -baseout TRIM/SS.11.33.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.34_1.fq.gz reads/SS.11.34_2.fq.gz -baseout TRIM/SS.11.34.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.35_1.fq.gz reads/SS.11.35_2.fq.gz -baseout TRIM/SS.11.35.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.36_1.fq.gz reads/SS.11.36_2.fq.gz -baseout TRIM/SS.11.36.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.37_1.fq.gz reads/SS.11.37_2.fq.gz -baseout TRIM/SS.11.37.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.38_1.fq.gz reads/SS.11.38_2.fq.gz -baseout TRIM/SS.11.38.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.39_1.fq.gz reads/SS.11.39_2.fq.gz -baseout TRIM/SS.11.39.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.40_1.fq.gz reads/SS.11.40_2.fq.gz -baseout TRIM/SS.11.40.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.41_1.fq.gz reads/SS.11.41_2.fq.gz -baseout TRIM/SS.11.41.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.42_1.fq.gz reads/SS.11.42_2.fq.gz -baseout TRIM/SS.11.42.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.43_1.fq.gz reads/SS.11.43_2.fq.gz -baseout TRIM/SS.11.43.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.44_1.fq.gz reads/SS.11.44_2.fq.gz -baseout TRIM/SS.11.44.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.45_1.fq.gz reads/SS.11.45_2.fq.gz -baseout TRIM/SS.11.45.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.46_1.fq.gz reads/SS.11.46_2.fq.gz -baseout TRIM/SS.11.46.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.47_1.fq.gz reads/SS.11.47_2.fq.gz -baseout TRIM/SS.11.47.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.48_1.fq.gz reads/SS.11.48_2.fq.gz -baseout TRIM/SS.11.48.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.49_1.fq.gz reads/SS.11.49_2.fq.gz -baseout TRIM/SS.11.49.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.50_1.fq.gz reads/SS.11.50_2.fq.gz -baseout TRIM/SS.11.50.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.51_1.fq.gz reads/SS.11.51_2.fq.gz -baseout TRIM/SS.11.51.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.52_1.fq.gz reads/SS.11.52_2.fq.gz -baseout TRIM/SS.11.52.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.53_1.fq.gz reads/SS.11.53_2.fq.gz -baseout TRIM/SS.11.53.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.54_1.fq.gz reads/SS.11.54_2.fq.gz -baseout TRIM/SS.11.54.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.55_1.fq.gz reads/SS.11.55_2.fq.gz -baseout TRIM/SS.11.55.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36

<commit_msg>update trimming<commit_after>trimmomatic PE -phred33 reads/SS.11.01_1.fq.gz reads/SS.11.01_2.fq.gz -baseout TRIM/SS.11.01.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.02_1.fq.gz reads/SS.11.02_2.fq.gz -baseout TRIM/SS.11.02.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.03_1.fq.gz reads/SS.11.03_2.fq.gz -baseout TRIM/SS.11.03.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.04_1.fq.gz reads/SS.11.04_2.fq.gz -baseout TRIM/SS.11.04.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.05_1.fq.gz reads/SS.11.05_2.fq.gz -baseout TRIM/SS.11.05.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.06_1.fq.gz reads/SS.11.06_2.fq.gz -baseout TRIM/SS.11.06.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.07_1.fq.gz reads/SS.11.07_2.fq.gz -baseout TRIM/SS.11.07.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.08_1.fq.gz reads/SS.11.08_2.fq.gz -baseout TRIM/SS.11.08.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.09_1.fq.gz reads/SS.11.09_2.fq.gz -baseout TRIM/SS.11.09.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.10_1.fq.gz reads/SS.11.10_2.fq.gz -baseout TRIM/SS.11.10.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.11_1.fq.gz reads/SS.11.11_2.fq.gz -baseout TRIM/SS.11.11.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.12_1.fq.gz reads/SS.11.12_2.fq.gz -baseout TRIM/SS.11.12.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.13_1.fq.gz reads/SS.11.13_2.fq.gz -baseout TRIM/SS.11.13.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.14_1.fq.gz reads/SS.11.14_2.fq.gz -baseout TRIM/SS.11.14.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.15_1.fq.gz reads/SS.11.15_2.fq.gz -baseout TRIM/SS.11.15.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.16_1.fq.gz reads/SS.11.16_2.fq.gz -baseout TRIM/SS.11.16.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.17_1.fq.gz reads/SS.11.17_2.fq.gz -baseout TRIM/SS.11.17.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.18_1.fq.gz reads/SS.11.18_2.fq.gz -baseout TRIM/SS.11.18.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.19_1.fq.gz reads/SS.11.19_2.fq.gz -baseout TRIM/SS.11.19.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.20_1.fq.gz reads/SS.11.20_2.fq.gz -baseout TRIM/SS.11.20.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.21_1.fq.gz reads/SS.11.21_2.fq.gz -baseout TRIM/SS.11.21.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.22_1.fq.gz reads/SS.11.22_2.fq.gz -baseout TRIM/SS.11.22.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.23_1.fq.gz reads/SS.11.23_2.fq.gz -baseout TRIM/SS.11.23.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.24_1.fq.gz reads/SS.11.24_2.fq.gz -baseout TRIM/SS.11.24.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.25_1.fq.gz reads/SS.11.25_2.fq.gz -baseout TRIM/SS.11.25.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.26_1.fq.gz reads/SS.11.26_2.fq.gz -baseout TRIM/SS.11.26.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.27_1.fq.gz reads/SS.11.27_2.fq.gz -baseout TRIM/SS.11.27.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.28_1.fq.gz reads/SS.11.28_2.fq.gz -baseout TRIM/SS.11.28.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.29_1.fq.gz reads/SS.11.29_2.fq.gz -baseout TRIM/SS.11.29.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.30_1.fq.gz reads/SS.11.30_2.fq.gz -baseout TRIM/SS.11.30.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.31_1.fq.gz reads/SS.11.31_2.fq.gz -baseout TRIM/SS.11.31.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.32_1.fq.gz reads/SS.11.32_2.fq.gz -baseout TRIM/SS.11.32.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.33_1.fq.gz reads/SS.11.33_2.fq.gz -baseout TRIM/SS.11.33.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.34_1.fq.gz reads/SS.11.34_2.fq.gz -baseout TRIM/SS.11.34.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.35_1.fq.gz reads/SS.11.35_2.fq.gz -baseout TRIM/SS.11.35.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.36_1.fq.gz reads/SS.11.36_2.fq.gz -baseout TRIM/SS.11.36.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.37_1.fq.gz reads/SS.11.37_2.fq.gz -baseout TRIM/SS.11.37.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.38_1.fq.gz reads/SS.11.38_2.fq.gz -baseout TRIM/SS.11.38.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.39_1.fq.gz reads/SS.11.39_2.fq.gz -baseout TRIM/SS.11.39.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.40_1.fq.gz reads/SS.11.40_2.fq.gz -baseout TRIM/SS.11.40.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.41_1.fq.gz reads/SS.11.41_2.fq.gz -baseout TRIM/SS.11.41.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.42_1.fq.gz reads/SS.11.42_2.fq.gz -baseout TRIM/SS.11.42.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.43_1.fq.gz reads/SS.11.43_2.fq.gz -baseout TRIM/SS.11.43.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.44_1.fq.gz reads/SS.11.44_2.fq.gz -baseout TRIM/SS.11.44.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.45_1.fq.gz reads/SS.11.45_2.fq.gz -baseout TRIM/SS.11.45.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.46_1.fq.gz reads/SS.11.46_2.fq.gz -baseout TRIM/SS.11.46.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.47_1.fq.gz reads/SS.11.47_2.fq.gz -baseout TRIM/SS.11.47.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.48_1.fq.gz reads/SS.11.48_2.fq.gz -baseout TRIM/SS.11.48.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.49_1.fq.gz reads/SS.11.49_2.fq.gz -baseout TRIM/SS.11.49.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.50_1.fq.gz reads/SS.11.50_2.fq.gz -baseout TRIM/SS.11.50.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.51_1.fq.gz reads/SS.11.51_2.fq.gz -baseout TRIM/SS.11.51.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.52_1.fq.gz reads/SS.11.52_2.fq.gz -baseout TRIM/SS.11.52.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.53_1.fq.gz reads/SS.11.53_2.fq.gz -baseout TRIM/SS.11.53.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.54_1.fq.gz reads/SS.11.54_2.fq.gz -baseout TRIM/SS.11.54.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36
trimmomatic PE -phred33 reads/SS.11.55_1.fq.gz reads/SS.11.55_2.fq.gz -baseout TRIM/SS.11.55.fq.gz ILLUMINACLIP:/util/opt/anaconda/2.0/envs/trimmomatic-0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:36


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