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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Community rating: ?????

Converts .SFF sequence files to fastq format.

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 -> sff2fastq.

Input File(s)

Use FFGLB5S04.sff 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 (except in this case, the output file name was changed to FFGLB5S04tr.fq.

Output File(s)

Expect a fastq file as output. For the test case, the output file you will find in the example_data directory is named FFGLB5S04tr.fq.

Because sff files normally contain information about the raw sequences, trimming is normally part of the conversion process. Trimming can be turned off by setting trimming to off.

 Tool Source for App

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  1. ★★★★☆ Worked perfectly with Roche output files. De novo assembler version 2.7 (by hoytpr)

  2. ★★★★★ Runs quick and without flaws (by jontrip247)