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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Fastq-screen-0.4.4 Community rating: ?????

Screens fastq files against specific databases for contaminants or alternate sequences.

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 -> fastq_screen

Input File(s)

Use testdata.fq and the genomes directory from the directory above as test input. For running your own data, the bowtie2 index(es) must be contained in a directory named genomes, and the indexes must be named genome1, genome2, genome3 etc.

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.

 

Output File(s)

Expect a text file named after the input files as output. For the test case, the output files you will find in the example_data directory are named testdata_screen.png and testdata_screen.txt.

Tool Source for App

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