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