The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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All files are located in the Community Data directory of the iPlant Discovery Environment at the following path: Community Data > iplantcollaborative > example_data > trimmomatic-0.33 > inputs (/iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs)

  1. Paired-end reads: Select the files from the directory - /iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs/testfiles
    1. FASTQ Files (Read 1) - EP1_C1_CGATGT_L004_R1_001.fq.gz, sample_1_R1_001.fq.gz and sample_2_R1_001.fq.gz
    2. FASTQ Files (Read 2) - EP1_C1_CGATGT_L004_R2_001.fq.gz, sample_1_R2_001.fq.gz and sample_2_R2_001.fq.gz

  2. Single end reads

  3. Trimer file (Mandatory) - /iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs/testfile_trimmomatic.txt

  4. Adapters (Optional)
    1. ILLUMINACLIP adapter sequence file - /iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs/Adapters.fa
    2. Adapter clip seed mismatches (Default is 2) - Leave 
    3. Adapter clip palindrome clip threshold (Default is 30)
    4. Adapter clip simple clip threshold (Default is 10)
  5. Settings
    1. Phred33 (Default is Phred 64)
    2. Number of CPUs (Default is 4)
  6. Output
    1. Output Folder name (Default is trimout)