Development and Deployment of a Sequencing and Bioinformatics Pipeline for Rapid Detection of Structural Variations in Crop Genomes
College: Agricultural, Consumer and Environmental Sciences
Award year: 2014-2015
Crop plants have genomes as large and complex as the human genome—in some cases larger and more complex. However, almost all bioinformatics tools currently available to characterize Variants from high-throughput sequencing data are written for the human genome. Crop genomes are different and present different challenges, in particular because of current or ancestral polyploidy, inbreeding, use of hybrid lines and the types of repeats and transposons present. The project will develop a variant calling pipeline that uses high-performance computing resources to rapidly and accurately call all the major types of variant responsible for valuable traits in crops, based on high-throughput sequence data. At the end of the project a cross-platform, open-source package will be published for the crop science community.