Project Number: 6066-21310-005-26-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2017
End Date: Sep 1, 2021

Objective:
Develop software to assist in next-generation sequence analysis with applications to plant and animal genetics. The main emphasis will be on developing a next generation QTL mapping pipeline for improved genetic resolution. Additional projects in service of this objective will potentially involve routine bioinformatic analysis and user-interface development.

Approach:
The following approaches will serve to address the objective described above: 1. Develop simulation software using pre-existing R packages and custom programs in order to assist in experimental design of sequencing reactions. 2. Develop amplicon design software to facilitate QTL identification. 3. Develop variant effect prediction software. 4. Assist in RNA-seq, genome assembly, genotyping, and genetic analysis. 5. Develop front-end tools to make these softwares more useful to the community at large.