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:
Paired-end or Single-end (Mandatory)
- Enter a folder of sequencing files (Mandatory)
Trimmer settings file in text format (Mandatory)
- ILLUMINACLIP adapter sequence file (Optional)
Run Trimmomatic-programmable-0.36 as following:
Paired-end or Single-end (Mandatory) - single-end
- Enter a folder of sequencing files (Mandatory) - /iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs/testfiles
Trimmer settings file in text format (Mandatory) - /iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs/testfile_trimmomatic.txt
ILLUMINACLIP adapter sequence file (Optional) - /iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs/Adapters.fa
- 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 firstname.lastname@example.org. Thank you.