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 with user genome

Community rating: ?????

Automatic workflow for genotyping by sequencing analysis with user genome

Quick Start

Test Data


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 folder and 61VBPAAXX_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.
  • Select your own reference genome in Fasta format under "gbsBWA - Input data"

Output File(s)

Expect multiple folders and files as output. For the test case, the output folder under example_data directory contains 7 folders and 14 files.

Folders are:

  • fit
  • logs
  • mergedSNPs
  • mergedTBT
  • tagCounts
  • tbt
  • unfit

Files are:

  • bwa_output.sam
  • myMasterTags.cnt
  • myMasterTags.fasq.fq
  • myMasterTags.topm.bin
  • myMasterTags.topm.bin.log
  • temp1.sai
  • 8 *.fa.* index files

Tool Source for App

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  1. ☆☆☆☆☆ Why do I have to set the number of chromosomes on so many tabs? Can't I just set a global number? (by mgttri)

  2. ☆☆☆☆☆ Thanks so much for building this. There are pieces I would like to add...

    My one annoyance with working with this workflow is that I have to enter the number of chromosomes on so very many tabs. (by mgttri)

  3. The workflow is created by linking multiple apps together. These apps can run separately in case user wants to test another set of parameters for one of the steps. Therefore, it is necessary to specify chromosomes for each app.

    However, this can be improved if the workflow engine can pass the values of parameters from one app to another. So far this is not supported.