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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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)

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      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)

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    4. ILLUMINACLIP adapter sequence file (Optional) 

Test Data

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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)

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.

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