Kim, S. et al. Nat. Commun. 8, 13919 (2017).
As the bottom continues to drop on the cost of sequencing, the bottleneck for high-throughput studies moves upstream to sample preparation. Kim et al. addressed this problem for microbial genome sequencing by designing a microfluidic chip that fully integrates every step after sample input, including DNA extraction, library preparation and size selection. Each chip can process 96 samples, and the small reaction volumes lower reagent costs substantially and make it possible to accept up to 100-fold lower input while obtaining data quality that matches or exceeds that of standard library preparations. The researchers demonstrate this chip's utility for shotgun sequencing of microcolonies derived from soil samples, as well as for single-nucleotide-polymorphism analysis for hundreds of clinical isolates of Pseudomonas aeruginosa. In the future, the approach should be adaptable to different library preparation workflows.