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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This is the quality-based trimming program with SolexaQA. It should work with Illumina reads, but probably also 454 and Ion Torrent reads.

Quick Start

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> DynamicTrim

Input File(s)

Use FFGLB5S04.fastq from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Default parameters only, no further configuration needed. The application will try to determine the quality format of the reads. Sometimes setting the type of read manually is necessary under options. Values for probability or minimal quality can be set, also, as well as BWA trimming can be used.

Output File(s)

Expect a fastq file, the input file name plus ".trimmed" as output. For the test case, the output file you will find in the example_data directory is named FFGLB5S04.fastq.trimmed.

Tool Source for App

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