iPlant Collaborator: Accelerating Livestock Genomics With iAnimal

Next generation sequencing (NGS) data are revolutionizing livestock genomics, but also overwhelming current computing resources. Our research group has developed NGS pipelines at iAnimal to facilitate cutting-edge research in livestock. We’ve partnered with the 1000 bulls project, the Buffalo genome project, and several groups working in RNAseq and variant discovery in cattle, chickens, and pigs to expedite computation and facilitate the use of existing NGS methodologies. Critical resources at iAnimal include HPC resources, simplified user interfaces, fast data transfer, and personal interaction with biologists and computer scientists. Initial work has led to the development of a variant calling pipeline, and integration of existing RNAseq software (tophat and cufflinks) for livestock species. Future efforts are underway to develop a complete RNAseq pipeline and methods to analyze allele specific expression in livestock. As a proof of principal, the genotyping pipeline was used to call 18.4 million variants (Q20+) from 20 animals (9X to 30X) from the 1000 bulls project and 13.8 million SNPs in the water buffalo for the Buffalo genome consortium. We have assisted several groups in the livestock community with variant discovery, comparing methylation levels and RNAseq analysis in a variety of species. The development of iAnimal has provided livestock genomics groups with new resources to analyze and share large datasets faster than ever before. Tools and pipelines are continuing to evolve and improve every day. We believe the cyber-infrastructure provided by iAnimal will accelerate research in livestock genomics, allowing researchers to focus on the biology over computational concerns.