One of the challenges for the team at the Earlham Institute is analyzing the wheat genome, which is five times larger than the human genome and replete with repetitive elements that are difficult to align. Since wheat is a staple diet for over 30% of the world’s population, the Earlham Institute is focused on improving yields to feed a growing population (estimates predict nine billion people worldwide by 2050), a goal made more difficult by the loss of agricultural land, increasing global temperatures, and pathogens that severely deplete wheat yield worldwide. By understanding the genomic building blocks of wheat and its diversity, the Earlham Institute can help breeders overcome some of these obstacles.
Accelerating genomic analysis remains one of the toughest challenges in life sciences research. All manner of optimizations are in use — disk streaming, optimized parallel files systems, algorithm tweaks, faster processors, and hardware accelerator — that succeed with varying results. Alignment against reference genomes is a fundamental task undertaken daily by Institute researchers. Efficiency gains were needed due to the high throughput of genomic data processed at the Earlham Institute, where sequence alignment is critical to many sequencing projects.