Genotyping By Sequencing Workflow

Genotyping By Sequencing Workflow

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Automatic workflow for genotyping by sequencing analysis (based on Tassel3.0.133_standalone_build-4.1.6).

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.

  • Use these parameters within the DE app interface:
    • Select Oryza_sativa (japonica) as reference genome under gbsBWA - Input data
    • Default parameters for other options
    • May change "Minimum unique read" under gbsTags - Options to smaller value (takes longer to run)

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 6 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

Tool Source for App