Sff2Fastq
Sff2Fastq
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Converts .SFF sequence files to fastq format.
Quick Start
- To use Sff2Fastq, import your data in ___ format.
- Resources: https://github.com/indraniel/sff2fastq
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.