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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Prinseq-lite

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Prinseq can be used to filter, format or trim genome and metagenomic sequence data. Here most settings are default with user specified input and outputs. Assumes input is unzipped fastq.

Manual Source: 

Quick Start

Test Data

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

Input File(s)

Use frag_2.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.

  • set the minimum quality mean to 15
  • enter the output file name, frag_prnsq_2.fq

Output File(s)

Expect a file named as set in the parameters as output. For the test case, the output file you will find in the example_data directory is named frag_prnsq_2.fq .

Tool Source for App

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