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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A trimmomatic app that you program with a simple text file.

 

Trimmomatic-programmable-0.33

Description and Quick Start

This 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

Test Data

/iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs 

Input File(s)

A folder of fastq sequencing files, a plain text file with trimmer settings entered line by line, and an optional file of adapter or primer sequences. 

Parameters Used in App. A basic input settings file can be found here:

 

Sample trimmer settings include:

HEADCROP:7

ILLUMINACLIP:Adapters.fa:2:30:10

SLIDINGWINDOW:4:15

MINLEN:45

Output File(s)

The output is a folder named trimout containing renamed fastq files with trimmed sequences.

References

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