GBS Workflow
GBS Workflow
Community rating: ?????
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
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.