NCM 2022: Portable genomics hackathon for pathogen detection: a practical application of adaptive sampling to engage undergraduate learning

Next-generation sequencing technologies have proven vital for genomic surveillance of pathogens. However, the ongoing pandemic has demonstrated there is a critical gap in understanding this information by the public. Increased educational opportunities are needed to help grow workforce capacity. Here, we used a multi-week workshop to engage undergraduate students in a practical application of next-generation sequencing using MinION. Students each built and ran a portable genomics device to simulate the detection of pathogens. Working with safe, non-pathogenic samples, they tested the ability of nanopore adaptive sampling to enrich a particular microbial mock community member. We found that adaptive sampling was enriched by target composition. Despite a drop in total sequencing yield, we found a 50% increase in target genome yield with adaptive sampling compared with a control. Learning surveys found a clear increase in the interest and understanding of genomics.