App Name

GBS Genotype By Sequencing (GBS) is a pipeline that analyzes the reduced representation libraries constructed from a highly-multiplexed system using the Illumina next-generation sequencing platform. Key components of this system are: reduced sample handling, few PCR and purification steps, no size fractionation and inexpensive barcoding. Restriction enzymes are used to reduce genome complexity and avoid the repetitive fraction of the genome.

Quick Start

• To use GBS, upload your sequence data, enzyme file and create the folders as shown in following test data.
• Resources: http://www.maizegenetics.net/gbs-bioinformatics

Test Data

Input File(s)

Test data can be found under data -> Community Data -> TtT_Workshop -> Intro_GWAS -> gbs from DE.

Parameters Used in App

When the app is run in the Discovery Environment, use the following page for parameters with the above input file(s) to get the output provided in the next section below.

• Genotype By Sequencing Pipeline

Output File(s)

Expect SNP file at the end of the pipeline under gbs/hapmap/filt/rice.mergedSNPs.filt.c+.hmp.txt.