Rationale:

Trimmomatic-programmable-0.36 app provides access to all trimmers that Trimmomatic can use. It uses a line-by-line text file for programming the trimming profile. Trimmomatic is commonly used for trimming stretches of sequences that are extraneous contaminants or of low quality. There are many trimmers available to use within a single run of Trimmomatic. For this app, using a trimmer only requires including it (with proper syntax) in the trimmer settings file..

Trimmomatic-programmable-0.36 is invoked using the following:

1. Settings

   1. Paired-end or Single-end (Mandatory)

      The Paired End files should contain reads that have extension _R1_001.fq.gz/_R2_001.fq.gz or _R1_001.fastq.gz/_R2_001.fastq.gz or _R1_001.fq/_R2_001.fq or _R1_001.fastq/_R2_001.fastq. If the files don't follow this convention, the app will fail with no output files.

   2. Enter a folder of sequencing files (Mandatory)

   3. Trimmer settings file in text format (Mandatory)
      

      Input below a trimmer file in basic text format. You can create one in the Data window by clicking on the File menu and choosing Create > Plain text file. Enter line by line all the trimmer settings you want to use with Trimmomatic. See http://www.usadellab.org/cms/?page=trimmomatic for more details

   4. ILLUMINACLIP adapter sequence file (Optional) 

Test Data

Run Trimmomatic-programmable-0.36 as following:

1. Settings

   1. Paired-end or Single-end (Mandatory) - single-end

   2. Enter a folder of sequencing files (Mandatory) - /iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs/testfiles

   3. Trimmer settings file in text format (Mandatory) - /iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs/testfile_trimmomatic.txt

   4. ILLUMINACLIP adapter sequence file (Optional) - /iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs/Adapters.fa

2. Output
   1. trim_out folder containing the following files - trimSEP1_C1_CGATGT_L004_R1_001.fq.gz and trimSEP1_C1_CGATGT_L004_R2_001.fq.gz 

Please work through the documentation and add your comments on the bottom of this page, or email comments to support@cyverse.org. Thank you.