Workflows developed by Lindsay Clark at the Roy J. Carver Biotechnology Center at the University of Illinois, Urbana-Champaign. Funding is through the Excellence in Breeding program and CGIAR centers.
These workflows were developed to assist in KASP assay design from resequencing data in crop species. They can identify markers well-suited to particular tasks (pedigree verification, marker-assisted selection) and output the markers in a format that can be supplied directly to a vendor for KASP assay development. Flanking sequence 50 bp to either side of the SNP is output, and other SNPs in the region are annotated.
Each workflow is provided here in two formats. The one ending in .Rmd is the
one that you will edit and use to run the code. The one ending in .md is
intended to be easily readable from GitHub, and you can click on it from your
web browser to get a preview of what the workflow and results look like.
If you have a GitHub account and want to modify the workflows for use in your species of interest, I suggest making your own fork of this repository. If not, don't worry, you can always save a copy and edit it locally!
In RStudio, go to
File --> New Project --> Version Control --> Git
If you don't see an option for Git, follow these instructions to install it.
If you aren't making your own fork, put https://github.com/HPCBio/eib-marker-design in the "Repository URL" box. If you did make your own fork, put the URL for your fork there instead. Change the directory if you want, then click "Create Project". If you are successful, all of the files and directories from this repository will be copied to your computer and opened as an RStudio project.
Put your VCF and reference genome FASTA into the data directory. The results
directory is where the output will be after you run the code.