0.36 A flexible read trimming tool for Illumina NGS data Bolger, A. M., Lohse, M., and Usadel, B Phylogeny / Alignment http://www.usadellab.org/cms/index.php?page=trimmomatic http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf trimmomatic_xsede pe_command perl $se_vs_pe eq "PE" perl "trimmomatic_expanse PE -threads 12" 0 pe_command2 perl $se_vs_pe eq "PE" perl "-trimlog trim_log.txt inputfile1.fq.gz inputfile2.fq.gz" 2 se_command Queue perl $se_vs_pe eq "SE" perl "trimmomatic_wrapper SE -threads 12" 0 se_command2 Queue perl $se_vs_pe eq "SE" perl "-trimlog trim_log.txt inputfile1.fq.gz" 2 inputfile1 Input Sequence 1(fq) inputfile1.fq.gz runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 0.25 Estimate the maximum time your job will need to run. We recommend testimg initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. Maximum Hours to Run must be less than 168 perl $runtime > 168.0 Maximum Hours to Run must be greater than 0.1 perl $runtime < 0.1 The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hours perl $runtime ne 0 perl "runhours=$value\\n" trimmomatic_scheduler scheduler.conf perl "threads_per_process=12\\n" . "mem=23G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 se_vs_pe Single-end reads or Paired-end reads? SE Single-end Reads PE Paired-end Reads PE phred phred perl " -phred$value" 33 33 64 64 33 1 inputfile2 Input Sequence 2 (fq) perl $se_vs_pe eq "PE" inputfile2.fq.gz 3 pairedoutput1 paired output 1 filename perl $se_vs_pe eq "PE" perl "$value" paired_output_1.txt 6 unpairedoutput1 unpaired output 1 filename perl $se_vs_pe eq "PE" perl "$value" unpaired_output_1.txt 7 pairedoutput2 paired output 2 filename perl $se_vs_pe eq "PE" perl "$value" paired_output_2.txt 8 unpairedoutput2 unpaired output 2 filename perl $se_vs_pe eq "PE" perl "$value" unpaired_output_2.txt 9 seoutput1 single end output perl $se_vs_pe eq "SE" perl "$value" se_output_1.txt 8 leading LEADING 30 perl "LEADING:$value" 10 trailing TRAILING 30 perl " TRAILING:$value" 11 slidingwindowsize SLIDINGWINDOW windowSize 12 4 requiredQuality SLIDINGWINDOW requiredQuality perl " SLIDINGWINDOW:$slidingwindowsize:$value" 20 13 minlen MINLEN perl " MINLEN:$value" 36 14 all_outputfiles *