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Python Script ( Eric Normandeau Github:enormandeau) that re-synchronises paired fastq files that have become out of synch due to manipulation (e.g. trimming, filtering)

Quick Start

  • To use fastqCombinePairedEnd, import your data in fastq format.

Test Data

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

Input File(s)

Use shortjump_1.fastq and shortjump_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 spacer to "/"

Expect output files named after inputs as output. For the test case, the output files you will find in the example_data directory are named

shortjump_1.fastq_pairs_R1.fastq  shortjump_2.fastq_pairs_R2.fastq shortjump_1.fastq_pairs_singles.fastq

Tool Source for App