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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GBS Workflow

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Automatic workflow for Genotyping By Sequencing analysis

Quick Start

  • To use GBS Workflow, import your read data in qseq (preferred) or fastq format and provide an enzyme file for demultiplexing.
  • Resources: TASSEL GBS

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 -> gbs_workflow -> input.

Input File(s)

Use qseq as input file folder and 61VBPAAXX_key.txt as key file from the directory above as test input for gbsTags_TASSEL 3.0.133.

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.

  • gbsTags_TASSEL 3.0.133 - Options
    • Select tag format - qseq
    • Select enzyme - ApekI
  • gbsAlign_BWA 0.5.9 - Input data Or upload your own genome sequence
    • Select to upload your own genome sequence. Data is in  Community Data -> iplantcollaborative -> example_data -> gbs_workflow -> input-> Oryza_sativa.IRGSP-1.0.20.dna.fa.gz
  • all other parameters can be left as default

Output File(s)

Expect multiple folders as output. For the test case, the example output is under Community Data -> iplantcollaborative -> example_data -> gbs_workflow -> output.

Tool Source for App

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