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Automatic workflow for Genotyping By Sequencing analysis
- 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 for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> gbs_workflow -> input.
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
Expect multiple folders as output. For the test case, the example output is under Community Data -> iplantcollaborative -> example_data -> gbs_workflow -> output.