GBS Workflow with user genome

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Automatic workflow for genotyping by sequencing analysis with user genome

Quick Start

To use GBS Workflow with user genome, import your data in qseq or fastq format.
Resources: http://www.maizegenetics.net/tassel/

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

http://www.maizegenetics.net/tassel/