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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rePair-Fix Read Pairing

Community rating: ?????

Repairs paired read files that have lost pairing on some reads because of preprocessing.

Quick Start

  • To use rePair-Fix Read Pairing, import your data in fastq format. This app will likely work only with fastq files in older Illumina formats, e.g. pair names ending with \1.fastq and \2.fastq. 
  • Resources: https://sourceforge.net/projects/ngopt/

Test Data

Icon

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

Input File(s)

Use testqf_1.fastq and testqf_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.

  • Default parameters only, no further configuration needed.

Output File(s)

Expect 3 files named with input prefix as output. For the test case, the output files you will find in the example_data directory are named:

  testqfRPR_p1.fastq
  testqfRPR_p2.fastq
  testqfRPR_up.fastq
  testqfRPR_p1.fastq

  testqfRPR_p2.fastq

  testqfRPR_up.fastq

Tool Source for App

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