Sequencing Complex Genomes with PromethION Technology in a Core Setting

Many genomes are characterized by rearrangements confering novel phenotypes; including drug resistance, growth rate, desirable agricultural traits, and disease progression. Advances in long-read sequencing have shown that short-read approaches miss a many large, structural events. Until recently long-read sequencing has been limited in scope due the high costs and high input material requirements. The Oxford Nanopore PromethION offers a lower cost and lower starting material alterative to other long-read sequencing platforms. These changes will make long-read sequencing a more routine technology in genomic studies. At this time, CSHL has developed pipelines to rapidly sequence plant and human samples. To date we have completed >5 high coverage human genomes with per cell yield ~70Gb, and 100 plant genomes with yields ~90Gb. Our top yield has been >142Gb on a single cell. This work has allowed an in depth exploration of the structural events in cancer progression and plant breading characteristics. Despite these successes, integrating a PromethION in to core setting is a challenging prospect . Unlike other technologies, the system is not as robust to adjuncts that may be carried over from DNA extractions. This has the potential to require significant troubleshooting efforts that must be accounted for in the time and costs associated with projects. This is further compounded by variations in the flowcells themselves leading to uncertainly in the total data generated for a project. Another factor that much be considered is data management; as ~2Tb of data can be generated per flowcell. Basic data management methods like basecalling and data transmission can quickly overwhelm many data management systems. At this time CSHL is making plans for enhanced data storage and analysis systems to better enable large scale PromethION studies. This presentation will outline CSHL's experience with sequencing on the Oxford Nanopore PromethION and recommendations on best practices for a core facility.