As sequencing costs continue to drop, the upstream (library preparation) and downstream (data analysis & management) pieces of next-generation sequencing are becoming more important. The costs associated with library preparation have remained constant, so finding cost-saving modifications to this step has become increasingly important, especially at Gencove in our mission towards ubiquitous sequencing.
With increasing commercial options for library preparation kits available, choosing the correct kit for the job is critical. To address this methodological gap we have experimentally examined the performance of several library preparation kits in the context of low coverage whole genome sequencing (lcWGS) with imputation and built a resource for scientists choosing a library preparation kit for their next sequencing project
Our results show that the miniaturization of library prep protocols provides extensive cost savings without sacrificing imputation performance in lcWGS. Integrated DNA Technologies (IDT), Roche, and Illumina kits can be successfully miniaturized, and as the performance was approximately equivalent between kits, the decision of which to use will rely on whether full-length adapters are essential for PCR-free workflows, short time to prepare libraries is needed, or if you’re using long-read sequencing.
Our analysis provides a resource for scientists and decision-makers deciding between methods for lcWGS where cost is of importance.