Virginia-Type Peanut Genomic Tool Development

This repository stores the code used to develop the Virginia-Type peanut reference genome 'Bailey II' (NCBI JAGJTH000000000), and discover markers across the Bailey II genome. This work pertains to the following article: 'Newman, C. S., Andres, R. J., Youngblood, R. C., Campbell, J. D., Simpson, S. A., Cannon, S. B., Scheffler, B. E., Oakley, A. T., Hulse-Kemp, A. M., & Dunne, J. C. (2023). Initiation of genomics-assisted breeding in Virginia-type peanuts through the generation of a de novo reference genome and informative markers. Frontiers in Plant Science, 13. https://www.frontiersin.org/articles/10.3389/fpls.2022.1073542'. Please cite this work if you use this workflow in your research.

De Novo Genome Assembly

• Assembly

• Polishing

• Scaffolding

• Gap Filling

• Assess Quality

• Annotation

• GO Term Assignment

Marker Discovery

• Standard Short Variant Discovery Pipeline: Joint Calling

• Standard Variant Filtering

• Specialized Lenient Short Variant Calling & Filtering