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Trimmomatic-programmable-0.38

Trimmomatic-programmable-0.38

Apr 22, 2019

Rationale:



Trimmomatic-programmable-0.38 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-0.38 is invoked using the following:

  1. Paired-end reads:

    1. FASTQ Files (Read 1)

    2. FASTQ Files (Read 2)

  2. Single end reads

  3. Trimer file (Mandatory)

  4. Adapters (Optional)

    1. ILLUMINACLIP adapter sequence file

    2. Adapter clip seed mismatches (Default is 2)

    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)

Test Data

Run Trimmomatic-programmable-0.38 as following:

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)


Please work through the documentation and add your comments on the bottom of this page, or click the intercom button on this page. 

References