Pre-Process Reads

Illumina read quality control pipeline for paired and unpaired reads (maintains pairing)

Quick Start

To use Pre-Process Reads, import your data in fastq format.
Resources: https://github.com/jts/sga

Test Data

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

Input File(s)

Use frag_1.fastq, 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.

Use the default settings with frag_pr_preproc.fq as the name for the output.

Output File(s)

Expect a fastq file named according to the input name. For the test case, the output file you will find in the example_data directory is named frag_pr_preproc.fq.

Tool Source for App

https://github.com/jts/sga