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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UNEAK

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Universal Network Enabled Analysis Kit (UNEAK) is the non-reference Genotyping by Sequencing (GBS) SNP calling pipeline, which is an extension of the Java program of TASSEL

Quick Start

  • To use UNEAK, import your data in Fastq or Qseq format.
  • Resources: UNEAK Pipeline

Test Data

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

Input File(s)

Use illumina directory and OWB_KEY.txt 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 multiple folders as output. For the test case, the output older under example_data directory contains 8 folders.

Folders are:

  • hapMap
  • key
  • logs
  • mapinfo
  • mergedTagCounts
  • tagCounts
  • tagPair
  • tagsByTaxa

Tool Source for App

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