Development and Utilization of Bioinformatic Tools in Livestock Genomics

Whole genome sequence, SNPs, copy number variation, phenotypes and other “-omics” data underlie evidence-based estimations of an animal’s breeding value. Unfortunately, the computational resources (data storage, high-performance computing, analysis pipelines, etc.) that exploit this knowledge are limited in availability – many investigations are therefore restricted in their scope. Cyberinfrastructure developed by NRSP-8, and previous and present USDA-AFRI projects provide the livestock genomics community freely available platforms for the storage, sharing, analyses and comparison of large datasets – from genomes to phenotype data. These tools support a variety of genotype-phenotype related analyses in a platform that accommodates every level of user – from breeder to bioinformatician. These tools have been used to develop scalable, accessible versions of common workflows required for applying sequencing to livestock genomics.  Feedback from the livestock research community is requested to determine what additional resources are required.